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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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80
src/ASPHERE/compute_erotate_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -41,9 +41,9 @@ ComputeERotateAsphere(LAMMPS *lmp, int narg, char **arg) :
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_ellipsoid && !avec_line && !avec_tri)
if (!avec_ellipsoid && !avec_line && !avec_tri)
error->all(FLERR,"Compute erotate/asphere requires "
"atom style ellipsoid or line or tri");
"atom style ellipsoid or line or tri");
}
/* ---------------------------------------------------------------------- */
@ -67,7 +67,7 @@ void ComputeERotateAsphere::init()
if (line && line[i] >= 0) flag = 1;
if (tri && tri[i] >= 0) flag = 1;
if (!flag)
error->one(FLERR,"Compute erotate/asphere requires extended particles");
error->one(FLERR,"Compute erotate/asphere requires extended particles");
}
pfactor = 0.5 * force->mvv2e;
@ -106,53 +106,53 @@ double ComputeERotateAsphere::compute_scalar()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (ellipsoid && ellipsoid[i] >= 0) {
shape = ebonus[ellipsoid[i]].shape;
quat = ebonus[ellipsoid[i]].quat;
shape = ebonus[ellipsoid[i]].shape;
quat = ebonus[ellipsoid[i]].quat;
// principal moments of inertia
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
// principal moments of inertia
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
} else if (line && line[i] >= 0) {
length = lbonus[line[i]].length;
length = lbonus[line[i]].length;
erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * length*length*rmass[i] / 12.0;
erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * length*length*rmass[i] / 12.0;
} else if (tri && tri[i] >= 0) {
// principal moments of inertia
// principal moments of inertia
inertia[0] = tbonus[tri[i]].inertia[0];
inertia[1] = tbonus[tri[i]].inertia[1];
inertia[2] = tbonus[tri[i]].inertia[2];
inertia[0] = tbonus[tri[i]].inertia[0];
inertia[1] = tbonus[tri[i]].inertia[1];
inertia[2] = tbonus[tri[i]].inertia[2];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(tbonus[tri[i]].quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(tbonus[tri[i]].quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
}
MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar *= pfactor;
return scalar;

2
src/ASPHERE/compute_erotate_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

188
src/ASPHERE/compute_temp_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -76,7 +76,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
// error check
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
if (!avec)
error->all(FLERR,"Compute temp/asphere requires atom style ellipsoid");
}
@ -101,7 +101,7 @@ void ComputeTempAsphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Compute temp/asphere requires extended particles");
error->one(FLERR,"Compute temp/asphere requires extended particles");
if (tempbias) {
int i = modify->find_compute(id_bias);
@ -154,7 +154,7 @@ void ComputeTempAsphere::dof_compute()
int count = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tbias->dof_remove(i)) count++;
if (tbias->dof_remove(i)) count++;
int count_all;
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof -= nper*count_all;
@ -187,7 +187,7 @@ double ComputeTempAsphere::compute_scalar()
double *shape,*quat;
double wbody[3],inertia[3];
double rot[3][3];
// sum translational and rotational energy for each particle
// no point particles since divide by inertia
@ -196,52 +196,52 @@ double ComputeTempAsphere::compute_scalar()
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
// principal moments of inertia
// principal moments of inertia
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// principal moments of inertia
// principal moments of inertia
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
t += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
}
@ -287,71 +287,71 @@ void ComputeTempAsphere::compute_vector()
if (mode == ALL) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
// principal moments of inertia
massone = rmass[i];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
// principal moments of inertia
inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
// rotational kinetic energy
t[0] += inertia[0]*wbody[0]*wbody[0];
t[1] += inertia[1]*wbody[1]*wbody[1];
t[2] += inertia[2]*wbody[2]*wbody[2];
t[3] += inertia[0]*wbody[0]*wbody[1];
t[4] += inertia[1]*wbody[0]*wbody[2];
t[5] += inertia[2]*wbody[1]*wbody[2];
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
// rotational kinetic energy
t[0] += inertia[0]*wbody[0]*wbody[0];
t[1] += inertia[1]*wbody[1]*wbody[1];
t[2] += inertia[2]*wbody[2]*wbody[2];
t[3] += inertia[0]*wbody[0]*wbody[1];
t[4] += inertia[1]*wbody[0]*wbody[2];
t[5] += inertia[2]*wbody[1]*wbody[2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// principal moments of inertia
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
massone = rmass[i];
// principal moments of inertia
inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
// rotational kinetic energy
t[0] += inertia[0]*wbody[0]*wbody[0];
t[1] += inertia[1]*wbody[1]*wbody[1];
t[2] += inertia[2]*wbody[2]*wbody[2];
t[3] += inertia[0]*wbody[0]*wbody[1];
t[4] += inertia[1]*wbody[0]*wbody[2];
t[5] += inertia[2]*wbody[1]*wbody[2];
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
massone = rmass[i];
inertia[0] = INERTIA*massone * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*massone * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*massone * (shape[0]*shape[0]+shape[1]*shape[1]);
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
// rotational kinetic energy
t[0] += inertia[0]*wbody[0]*wbody[0];
t[1] += inertia[1]*wbody[1]*wbody[1];
t[2] += inertia[2]*wbody[2]*wbody[2];
t[3] += inertia[0]*wbody[0]*wbody[1];
t[4] += inertia[1]*wbody[0]*wbody[2];
t[5] += inertia[2]*wbody[1]*wbody[2];
}
}

2
src/ASPHERE/compute_temp_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

12
src/ASPHERE/fix_nh_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -35,7 +35,7 @@ FixNHAsphere::FixNHAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
if (!avec)
error->all(FLERR,"Compute nvt/nph/npt asphere requires atom style ellipsoid");
}
@ -53,7 +53,7 @@ void FixNHAsphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix nvt/nph/npt asphere requires extended particles");
error->one(FLERR,"Fix nvt/nph/npt asphere requires extended particles");
FixNH::init();
}
@ -76,7 +76,7 @@ void FixNHAsphere::nve_v()
// update angular momentum by 1/2 step for all particles
for (int i = 0; i < nlocal; i++) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] += dtf*torque[i][0];
angmom[i][1] += dtf*torque[i][1];
@ -127,7 +127,7 @@ void FixNHAsphere::nve_x()
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
@ -152,7 +152,7 @@ void FixNHAsphere::nh_v_temp()
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] *= factor_eta;
angmom[i][1] *= factor_eta;

2
src/ASPHERE/fix_nh_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

6
src/ASPHERE/fix_nph_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -38,7 +38,7 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@ -56,7 +56,7 @@ FixNPHAsphere::FixNPHAsphere(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";

2
src/ASPHERE/fix_nph_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

6
src/ASPHERE/fix_npt_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -38,7 +38,7 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
@ -56,7 +56,7 @@ FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";

2
src/ASPHERE/fix_npt_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

12
src/ASPHERE/fix_nve_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -34,11 +34,11 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
if (!avec)
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
}
@ -56,7 +56,7 @@ void FixNVEAsphere::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix nve/asphere requires extended particles");
error->one(FLERR,"Fix nve/asphere requires extended particles");
FixNVE::init();
}
@ -96,7 +96,7 @@ void FixNVEAsphere::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
// update angular momentum by 1/2 step
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
@ -140,7 +140,7 @@ void FixNVEAsphere::final_integrate()
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];

2
src/ASPHERE/fix_nve_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

12
src/ASPHERE/fix_nve_asphere_noforce.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -38,7 +38,7 @@ FixNVEAsphereNoforce::FixNVEAsphereNoforce(LAMMPS *lmp, int narg, char **arg) :
// error check
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!atom->ellipsoid_flag)
if (!atom->ellipsoid_flag)
error->all(FLERR,"Fix nve/asphere/noforce requires atom style ellipsoid");
}
@ -59,7 +59,7 @@ void FixNVEAsphereNoforce::init()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix nve/asphere/noforce requires extended particles");
error->one(FLERR,"Fix nve/asphere/noforce requires extended particles");
}
/* ---------------------------------------------------------------------- */
@ -94,15 +94,15 @@ void FixNVEAsphereNoforce::initial_integrate(int vflag)
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
MathExtra::richardson(quat,angmom[i],omega,inertia,dtq);
}

4
src/ASPHERE/fix_nve_asphere_noforce.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -29,7 +29,7 @@ class FixNVEAsphereNoforce : public FixNVENoforce {
FixNVEAsphereNoforce(class LAMMPS *, int, char **);
void initial_integrate(int);
void init();
private:
double dtq;
class AtomVecEllipsoid *avec;

4
src/ASPHERE/fix_nve_line.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -155,7 +155,7 @@ void FixNVELine::final_integrate()
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
length = bonus[line[i]].length;
dtirotate = dtfrotate / (length*length*rmass[i]);
omega[i][2] += dtirotate * torque[i][2];

2
src/ASPHERE/fix_nve_line.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

10
src/ASPHERE/fix_nve_tri.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -109,7 +109,7 @@ void FixNVETri::initial_integrate(int vflag)
x[i][2] += dtv * v[i][2];
// update angular momentum by 1/2 step
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
@ -119,9 +119,9 @@ void FixNVETri::initial_integrate(int vflag)
// returns new normalized quaternion
MathExtra::mq_to_omega(angmom[i],bonus[tri[i]].quat,
bonus[tri[i]].inertia,omega);
bonus[tri[i]].inertia,omega);
MathExtra::richardson(bonus[tri[i]].quat,angmom[i],omega,
bonus[tri[i]].inertia,dtq);
bonus[tri[i]].inertia,dtq);
}
}
@ -149,7 +149,7 @@ void FixNVETri::final_integrate()
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];

2
src/ASPHERE/fix_nve_tri.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

4
src/ASPHERE/fix_nvt_asphere.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -37,7 +37,7 @@ FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];

2
src/ASPHERE/fix_nvt_asphere.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

266
src/ASPHERE/pair_gayberne.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -99,7 +99,7 @@ void PairGayBerne::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -135,81 +135,81 @@ void PairGayBerne::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
default:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (newton_pair || j < nlocal) {
rtor[0] *= factor_lj;
rtor[1] *= factor_lj;
rtor[2] *= factor_lj;
rtor[1] *= factor_lj;
rtor[2] *= factor_lj;
f[j][0] -= fforce[0];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
f[j][1] -= fforce[1];
f[j][2] -= fforce[2];
tor[j][0] += rtor[0];
tor[j][1] += rtor[1];
tor[j][2] += rtor[2];
tor[j][1] += rtor[1];
tor[j][2] += rtor[2];
}
if (eflag) evdwl = factor_lj*one_eng;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}
@ -263,14 +263,14 @@ void PairGayBerne::settings(int narg, char **arg)
upsilon = force->numeric(arg[1])/2.0;
mu = force->numeric(arg[2]);
cut_global = force->numeric(arg[3]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@ -296,7 +296,7 @@ void PairGayBerne::coeff(int narg, char **arg)
double eja_one = force->numeric(arg[7]);
double ejb_one = force->numeric(arg[8]);
double ejc_one = force->numeric(arg[9]);
double cut_one = cut_global;
if (narg == 11) cut_one = force->numeric(arg[10]);
@ -307,18 +307,18 @@ void PairGayBerne::coeff(int narg, char **arg)
sigma[i][j] = sigma_one;
cut[i][j] = cut_one;
if (eia_one != 0.0 || eib_one != 0.0 || eic_one != 0.0) {
well[i][0] = pow(eia_one,-1.0/mu);
well[i][0] = pow(eia_one,-1.0/mu);
well[i][1] = pow(eib_one,-1.0/mu);
well[i][2] = pow(eic_one,-1.0/mu);
if (eia_one == eib_one && eib_one == eic_one) setwell[i] = 2;
else setwell[i] = 1;
well[i][2] = pow(eic_one,-1.0/mu);
if (eia_one == eib_one && eib_one == eic_one) setwell[i] = 2;
else setwell[i] = 1;
}
if (eja_one != 0.0 || ejb_one != 0.0 || ejc_one != 0.0) {
well[j][0] = pow(eja_one,-1.0/mu);
well[j][0] = pow(eja_one,-1.0/mu);
well[j][1] = pow(ejb_one,-1.0/mu);
well[j][2] = pow(ejc_one,-1.0/mu);
if (eja_one == ejb_one && ejb_one == ejc_one) setwell[j] = 2;
else setwell[j] = 1;
well[j][2] = pow(ejc_one,-1.0/mu);
if (eja_one == ejb_one && ejb_one == ejc_one) setwell[j] = 2;
else setwell[j] = 1;
}
setflag[i][j] = 1;
count++;
@ -349,7 +349,7 @@ void PairGayBerne::init_style()
shape2[i][0] = shape1[i][0]*shape1[i][0];
shape2[i][1] = shape1[i][1]*shape1[i][1];
shape2[i][2] = shape1[i][2]*shape1[i][2];
lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
sqrt(shape1[i][0]*shape1[i][1]);
}
}
@ -365,41 +365,41 @@ double PairGayBerne::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
int ishape = 0;
if (shape1[i][0] != shape1[i][1] ||
shape1[i][0] != shape1[i][2] ||
if (shape1[i][0] != shape1[i][1] ||
shape1[i][0] != shape1[i][2] ||
shape1[i][1] != shape1[i][2]) ishape = 1;
if (setwell[i] == 1) ishape = 1;
int jshape = 0;
if (shape1[j][0] != shape1[j][1] ||
shape1[j][0] != shape1[j][2] ||
if (shape1[j][0] != shape1[j][1] ||
shape1[j][0] != shape1[j][2] ||
shape1[j][1] != shape1[j][2]) jshape = 1;
if (setwell[j] == 1) jshape = 1;
if (ishape == 0 && jshape == 0)
form[i][i] = form[j][j] = form[i][j] = form[j][i] = SPHERE_SPHERE;
else if (ishape == 0) {
form[i][i] = SPHERE_SPHERE; form[j][j] = ELLIPSE_ELLIPSE;
form[i][j] = SPHERE_ELLIPSE; form[j][i] = ELLIPSE_SPHERE;
form[i][j] = SPHERE_ELLIPSE; form[j][i] = ELLIPSE_SPHERE;
} else if (jshape == 0) {
form[j][j] = SPHERE_SPHERE; form[i][i] = ELLIPSE_ELLIPSE;
form[j][i] = SPHERE_ELLIPSE; form[i][j] = ELLIPSE_SPHERE;
} else
form[j][i] = SPHERE_ELLIPSE; form[i][j] = ELLIPSE_SPHERE;
} else
form[i][i] = form[j][j] = form[i][j] = form[j][i] = ELLIPSE_ELLIPSE;
epsilon[j][i] = epsilon[i][j];
@ -696,9 +696,9 @@ double PairGayBerne::gayberne_analytic(const int i,const int j,double a1[3][3],
------------------------------------------------------------------------- */
double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
double b1[3][3],double g1[3][3],
double b1[3][3],double g1[3][3],
double *r12,const double rsq,double *fforce,
double *ttor)
double *ttor)
{
double tempv[3], tempv2[3];
double temp[3][3];
@ -713,9 +713,9 @@ double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
// compute distance of closest approach
double g12[3][3];
g12[0][0] = g1[0][0]+shape2[type[j]][0];
g12[1][1] = g1[1][1]+shape2[type[j]][0];
g12[2][2] = g1[2][2]+shape2[type[j]][0];
g12[0][0] = g1[0][0]+shape2[type[j]][0];
g12[1][1] = g1[1][1]+shape2[type[j]][0];
g12[2][2] = g1[2][2]+shape2[type[j]][0];
g12[0][1] = g1[0][1]; g12[1][0] = g1[1][0];
g12[0][2] = g1[0][2]; g12[2][0] = g1[2][0];
g12[1][2] = g1[1][2]; g12[2][1] = g1[2][1];
@ -750,9 +750,9 @@ double PairGayBerne::gayberne_lj(const int i,const int j,double a1[3][3],
double b12[3][3];
double iota[3];
b12[0][0] = b1[0][0] + well[type[j]][0];
b12[1][1] = b1[1][1] + well[type[j]][0];
b12[2][2] = b1[2][2] + well[type[j]][0];
b12[0][0] = b1[0][0] + well[type[j]][0];
b12[1][1] = b1[1][1] + well[type[j]][0];
b12[2][2] = b1[2][2] + well[type[j]][0];
b12[0][1] = b1[0][1]; b12[1][0] = b1[1][0];
b12[0][2] = b1[0][2]; b12[2][0] = b1[2][0];
b12[1][2] = b1[1][2]; b12[2][1] = b1[2][1];
@ -853,58 +853,58 @@ void PairGayBerne::compute_eta_torque(double m[3][3], double m2[3][3],
double den = m[1][0]*m[0][2]*m[2][1]-m[0][0]*m[1][2]*m[2][1]-
m[0][2]*m[2][0]*m[1][1]+m[0][1]*m[2][0]*m[1][2]-
m[1][0]*m[0][1]*m[2][2]+m[0][0]*m[1][1]*m[2][2];
ans[0][0] = s[0]*(m[1][2]*m[0][1]*m2[0][2]+2.0*m[1][1]*m[2][2]*m2[0][0]-
m[1][1]*m2[0][2]*m[0][2]-2.0*m[1][2]*m2[0][0]*m[2][1]+
m2[0][1]*m[0][2]*m[2][1]-m2[0][1]*m[0][1]*m[2][2]-
m[1][0]*m[2][2]*m2[0][1]+m[2][0]*m[1][2]*m2[0][1]+
m[1][0]*m2[0][2]*m[2][1]-m2[0][2]*m[2][0]*m[1][1])/den;
m[1][1]*m2[0][2]*m[0][2]-2.0*m[1][2]*m2[0][0]*m[2][1]+
m2[0][1]*m[0][2]*m[2][1]-m2[0][1]*m[0][1]*m[2][2]-
m[1][0]*m[2][2]*m2[0][1]+m[2][0]*m[1][2]*m2[0][1]+
m[1][0]*m2[0][2]*m[2][1]-m2[0][2]*m[2][0]*m[1][1])/den;
ans[0][1] = s[0]*(m[0][2]*m2[0][0]*m[2][1]-m[2][2]*m2[0][0]*m[0][1]+
2.0*m[0][0]*m[2][2]*m2[0][1]-m[0][0]*m2[0][2]*m[1][2]-
2.0*m[2][0]*m[0][2]*m2[0][1]+m2[0][2]*m[1][0]*m[0][2]-
m[2][2]*m[1][0]*m2[0][0]+m[2][0]*m2[0][0]*m[1][2]+
m[2][0]*m2[0][2]*m[0][1]-m2[0][2]*m[0][0]*m[2][1])/den;
2.0*m[0][0]*m[2][2]*m2[0][1]-m[0][0]*m2[0][2]*m[1][2]-
2.0*m[2][0]*m[0][2]*m2[0][1]+m2[0][2]*m[1][0]*m[0][2]-
m[2][2]*m[1][0]*m2[0][0]+m[2][0]*m2[0][0]*m[1][2]+
m[2][0]*m2[0][2]*m[0][1]-m2[0][2]*m[0][0]*m[2][1])/den;
ans[0][2] = s[0]*(m[0][1]*m[1][2]*m2[0][0]-m[0][2]*m2[0][0]*m[1][1]-
m[0][0]*m[1][2]*m2[0][1]+m[1][0]*m[0][2]*m2[0][1]-
m2[0][1]*m[0][0]*m[2][1]-m[2][0]*m[1][1]*m2[0][0]+
2.0*m[1][1]*m[0][0]*m2[0][2]-2.0*m[1][0]*m2[0][2]*m[0][1]+
m[1][0]*m[2][1]*m2[0][0]+m[2][0]*m2[0][1]*m[0][1])/den;
m[0][0]*m[1][2]*m2[0][1]+m[1][0]*m[0][2]*m2[0][1]-
m2[0][1]*m[0][0]*m[2][1]-m[2][0]*m[1][1]*m2[0][0]+
2.0*m[1][1]*m[0][0]*m2[0][2]-2.0*m[1][0]*m2[0][2]*m[0][1]+
m[1][0]*m[2][1]*m2[0][0]+m[2][0]*m2[0][1]*m[0][1])/den;
ans[1][0] = s[1]*(-m[1][1]*m2[1][2]*m[0][2]+2.0*m[1][1]*m[2][2]*m2[1][0]+
m[1][2]*m[0][1]*m2[1][2]-2.0*m[1][2]*m2[1][0]*m[2][1]+
m2[1][1]*m[0][2]*m[2][1]-m2[1][1]*m[0][1]*m[2][2]-
m[1][0]*m[2][2]*m2[1][1]+m[2][0]*m[1][2]*m2[1][1]-
m2[1][2]*m[2][0]*m[1][1]+m[1][0]*m2[1][2]*m[2][1])/den;
m[1][2]*m[0][1]*m2[1][2]-2.0*m[1][2]*m2[1][0]*m[2][1]+
m2[1][1]*m[0][2]*m[2][1]-m2[1][1]*m[0][1]*m[2][2]-
m[1][0]*m[2][2]*m2[1][1]+m[2][0]*m[1][2]*m2[1][1]-
m2[1][2]*m[2][0]*m[1][1]+m[1][0]*m2[1][2]*m[2][1])/den;
ans[1][1] = s[1]*(m[0][2]*m2[1][0]*m[2][1]-m[0][1]*m[2][2]*m2[1][0]+
2.0*m[2][2]*m[0][0]*m2[1][1]-m2[1][2]*m[0][0]*m[1][2]-
2.0*m[2][0]*m2[1][1]*m[0][2]-m[1][0]*m[2][2]*m2[1][0]+
m[2][0]*m[1][2]*m2[1][0]+m[1][0]*m2[1][2]*m[0][2]-
m[0][0]*m2[1][2]*m[2][1]+m2[1][2]*m[0][1]*m[2][0])/den;
2.0*m[2][2]*m[0][0]*m2[1][1]-m2[1][2]*m[0][0]*m[1][2]-
2.0*m[2][0]*m2[1][1]*m[0][2]-m[1][0]*m[2][2]*m2[1][0]+
m[2][0]*m[1][2]*m2[1][0]+m[1][0]*m2[1][2]*m[0][2]-
m[0][0]*m2[1][2]*m[2][1]+m2[1][2]*m[0][1]*m[2][0])/den;
ans[1][2] = s[1]*(m[0][1]*m[1][2]*m2[1][0]-m[0][2]*m2[1][0]*m[1][1]-
m[0][0]*m[1][2]*m2[1][1]+m[1][0]*m[0][2]*m2[1][1]+
2.0*m[1][1]*m[0][0]*m2[1][2]-m[0][0]*m2[1][1]*m[2][1]+
m[0][1]*m[2][0]*m2[1][1]-m2[1][0]*m[2][0]*m[1][1]-
2.0*m[1][0]*m[0][1]*m2[1][2]+m[1][0]*m2[1][0]*m[2][1])/den;
m[0][0]*m[1][2]*m2[1][1]+m[1][0]*m[0][2]*m2[1][1]+
2.0*m[1][1]*m[0][0]*m2[1][2]-m[0][0]*m2[1][1]*m[2][1]+
m[0][1]*m[2][0]*m2[1][1]-m2[1][0]*m[2][0]*m[1][1]-
2.0*m[1][0]*m[0][1]*m2[1][2]+m[1][0]*m2[1][0]*m[2][1])/den;
ans[2][0] = s[2]*(-m[1][1]*m[0][2]*m2[2][2]+m[0][1]*m[1][2]*m2[2][2]+
2.0*m[1][1]*m2[2][0]*m[2][2]-m[0][1]*m2[2][1]*m[2][2]+
m[0][2]*m[2][1]*m2[2][1]-2.0*m2[2][0]*m[2][1]*m[1][2]-
m[1][0]*m2[2][1]*m[2][2]+m[1][2]*m[2][0]*m2[2][1]-
m[1][1]*m[2][0]*m2[2][2]+m[2][1]*m[1][0]*m2[2][2])/den;
2.0*m[1][1]*m2[2][0]*m[2][2]-m[0][1]*m2[2][1]*m[2][2]+
m[0][2]*m[2][1]*m2[2][1]-2.0*m2[2][0]*m[2][1]*m[1][2]-
m[1][0]*m2[2][1]*m[2][2]+m[1][2]*m[2][0]*m2[2][1]-
m[1][1]*m[2][0]*m2[2][2]+m[2][1]*m[1][0]*m2[2][2])/den;
ans[2][1] = s[2]*-(m[0][1]*m[2][2]*m2[2][0]-m[0][2]*m2[2][0]*m[2][1]-
2.0*m2[2][1]*m[0][0]*m[2][2]+m[1][2]*m2[2][2]*m[0][0]+
2.0*m2[2][1]*m[0][2]*m[2][0]+m[1][0]*m2[2][0]*m[2][2]-
m[1][0]*m[0][2]*m2[2][2]-m[1][2]*m[2][0]*m2[2][0]+
m[0][0]*m2[2][2]*m[2][1]-m2[2][2]*m[0][1]*m[2][0])/den;
2.0*m2[2][1]*m[0][0]*m[2][2]+m[1][2]*m2[2][2]*m[0][0]+
2.0*m2[2][1]*m[0][2]*m[2][0]+m[1][0]*m2[2][0]*m[2][2]-
m[1][0]*m[0][2]*m2[2][2]-m[1][2]*m[2][0]*m2[2][0]+
m[0][0]*m2[2][2]*m[2][1]-m2[2][2]*m[0][1]*m[2][0])/den;
ans[2][2] = s[2]*(m[0][1]*m[1][2]*m2[2][0]-m[0][2]*m2[2][0]*m[1][1]-
m[0][0]*m[1][2]*m2[2][1]+m[1][0]*m[0][2]*m2[2][1]-
m[1][1]*m[2][0]*m2[2][0]-m[2][1]*m2[2][1]*m[0][0]+
2.0*m[1][1]*m2[2][2]*m[0][0]+m[2][1]*m[1][0]*m2[2][0]+
m[2][0]*m[0][1]*m2[2][1]-2.0*m2[2][2]*m[1][0]*m[0][1])/den;
m[0][0]*m[1][2]*m2[2][1]+m[1][0]*m[0][2]*m2[2][1]-
m[1][1]*m[2][0]*m2[2][0]-m[2][1]*m2[2][1]*m[0][0]+
2.0*m[1][1]*m2[2][2]*m[0][0]+m[2][1]*m[1][0]*m2[2][0]+
m[2][0]*m[0][1]*m2[2][1]-2.0*m2[2][2]*m[1][0]*m[0][1])/den;
}

10
src/ASPHERE/pair_gayberne.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -60,12 +60,12 @@ class PairGayBerne : public Pair {
void allocate();
double gayberne_analytic(const int i, const int j, double a1[3][3],
double a2[3][3], double b1[3][3], double b2[3][3],
double g1[3][3], double g2[3][3], double *r12,
const double rsq, double *fforce, double *ttor,
double g1[3][3], double g2[3][3], double *r12,
const double rsq, double *fforce, double *ttor,
double *rtor);
double gayberne_lj(const int i, const int j, double a1[3][3],
double b1[3][3],double g1[3][3],double *r12,
const double rsq, double *fforce, double *ttor);
double b1[3][3],double g1[3][3],double *r12,
const double rsq, double *fforce, double *ttor);
void compute_eta_torque(double m[3][3], double m2[3][3],
double *s, double ans[3][3]);
};

284
src/ASPHERE/pair_line_lj.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -88,12 +88,12 @@ void PairLineLJ::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// grow discrete list if necessary and initialize
if (nall > nmax) {
@ -116,7 +116,7 @@ void PairLineLJ::compute(int eflag, int vflag)
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
@ -126,179 +126,179 @@ void PairLineLJ::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
// line/line interactions = NxN particles
evdwl = 0.0;
if (line[i] >= 0 && line[j] >= 0) {
if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
npj = dnum[j];
jfirst = dfirst[j];
if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
npj = dnum[j];
jfirst = dfirst[j];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
torque[i][2] += dxi*fi[1] - dyi*fi[0];
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
torque[i][2] += dxi*fi[1] - dyi*fi[0];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
torque[j][2] += dxj*fj[1] - dyj*fj[0];
}
}
}
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
torque[j][2] += dxj*fj[1] - dyj*fj[0];
}
}
}
// line/particle interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[i] >= 0) {
if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
npi = dnum[i];
ifirst = dfirst[i];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xj[0] = x[j][0];
xj[1] = x[j][1];
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xj[0] = x[j][0];
xj[1] = x[j][1];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
torque[i][2] += dxi*fi[1] - dyi*fi[0];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
}
}
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
torque[i][2] += dxi*fi[1] - dyi*fi[0];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
}
}
// particle/line interaction = Nx1 particles
// convert line into Np particles based on sigma and line length
} else if (line[j] >= 0) {
if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
npj = dnum[j];
jfirst = dfirst[j];
if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
npj = dnum[j];
jfirst = dfirst[j];
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
xi[0] = x[i][0];
xi[1] = x[i][1];
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
xi[0] = x[i][0];
xi[1] = x[i][1];
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
rsq = delx*delx + dely*dely;
sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
if (newton_pair || j < nlocal) {
f[j][0] += fj[0];
f[j][1] += fj[1];
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
torque[j][2] += dxj*fj[1] - dyj*fj[0];
}
}
fi[0] = delx*fpair;
fi[1] = dely*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
if (newton_pair || j < nlocal) {
f[j][0] += fj[0];
f[j][1] += fj[1];
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
torque[j][2] += dxj*fj[1] - dyj*fj[0];
}
}
// particle/particle interaction = 1x1 particles
} else {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = forcelj*r2inv;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = forcelj*r2inv;
if (eflag)
evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (eflag)
evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
evdwl,0.0,fpair,delx,dely,delz);
}
}
@ -306,7 +306,7 @@ void PairLineLJ::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairLineLJ::allocate()
@ -331,7 +331,7 @@ void PairLineLJ::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairLineLJ::settings(int narg, char **arg)
@ -346,7 +346,7 @@ void PairLineLJ::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@ -356,7 +356,7 @@ void PairLineLJ::settings(int narg, char **arg)
void PairLineLJ::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@ -392,7 +392,7 @@ double PairLineLJ::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}

2
src/ASPHERE/pair_line_lj.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

62
src/ASPHERE/pair_resquared.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -35,8 +35,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairRESquared::PairRESquared(LAMMPS *lmp) : Pair(lmp),
b_alpha(45.0/56.0),
PairRESquared::PairRESquared(LAMMPS *lmp) : Pair(lmp),
b_alpha(45.0/56.0),
cr60(pow(60.0,1.0/3.0))
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
@ -103,7 +103,7 @@ void PairRESquared::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -133,7 +133,7 @@ void PairRESquared::compute(int eflag, int vflag)
// compute if less than cutoff
if (rsq < cutsq[itype][jtype]) {
fforce[0] = fforce[1] = fforce[2] = 0.0;
fforce[0] = fforce[1] = fforce[2] = 0.0;
switch (form[itype][jtype]) {
@ -197,9 +197,9 @@ void PairRESquared::compute(int eflag, int vflag)
if (eflag) evdwl = factor_lj*one_eng;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}
@ -250,7 +250,7 @@ void PairRESquared::settings(int narg, char **arg)
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
@ -283,7 +283,7 @@ void PairRESquared::coeff(int narg, char **arg)
double eja_one = force->numeric(arg[7]);
double ejb_one = force->numeric(arg[8]);
double ejc_one = force->numeric(arg[9]);
double cut_one = cut_global;
if (narg == 11) cut_one = force->numeric(arg[10]);
@ -348,12 +348,12 @@ double PairRESquared::init_one(int i, int j)
error->all(FLERR,"Pair resquared epsilon a,b,c coeffs are not all set");
int ishape = 0;
if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0)
if (shape1[i][0] != 0.0 && shape1[i][1] != 0.0 && shape1[i][2] != 0.0)
ishape = 1;
int jshape = 0;
if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0)
if (shape1[j][0] != 0.0 && shape1[j][1] != 0.0 && shape1[j][2] != 0.0)
jshape = 1;
if (ishape == 0 && jshape == 0) {
form[i][j] = SPHERE_SPHERE;
form[j][i] = SPHERE_SPHERE;
@ -384,12 +384,12 @@ double PairRESquared::init_one(int i, int j)
sigma[i][j] = sigma[j][i];
cut[i][j] = cut[j][i];
}
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
@ -513,7 +513,7 @@ void PairRESquared::precompute_i(const int i,RE2Vars &ws)
MathExtra::plus3(ws.lAsa[i],ws.lAtwo[i],ws.lAsa[i]);
}
}
/* ----------------------------------------------------------------------
Compute the derivative of the determinant of m, using m and the
derivative of m (m2)
@ -545,7 +545,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
double *rtor)
{
int *type = atom->type;
// pair computations for energy, force, torque
double z1[3],z2[3]; // A1*rhat # don't need to store
@ -568,7 +568,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
double sigh; // sigma/h12
double tprod; // eta*chi*sigh
double Ua,Ur; // attractive/repulsive parts of potential
// pair computations for force, torque
double sec; // sigma*eta*chi
@ -593,7 +593,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
double ddH; // derivative of det(H12)
double deta,dchi,dh12; // derivatives of eta,chi,h12
double dUr,dUa; // derivatives of Ua,Ur
// pair computations for torque
double fwae[3]; // -fourw'*aTe
@ -715,7 +715,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
hsec = h12+3.0*sec;
dspu = 1.0/h12-1.0/hsec+stemp;
pbsu = 3.0*sigma[type[i]][type[j]]/hsec;
stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+
1.0/(shape1[type[i]][1]*cr60+h12)+
1.0/(shape1[type[i]][2]*cr60+h12)+
@ -725,7 +725,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
hsec = h12+b_alpha*sec;
dspr = 7.0/h12-1.0/hsec+stemp;
pbsr = b_alpha*sigma[type[i]][type[j]]/hsec;
for (int i=0; i<3; i++) {
u[0] = -rhat[i]*rhat[0];
u[1] = -rhat[i]*rhat[1];
@ -757,7 +757,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
dUr = pbsr*(eta*dchi+deta*chi)-dh12*dspr;
fforce[i]=dUr*Ur+dUa*Ua;
}
// torque on i
MathExtra::vecmat(fourw,wi.aTe,fwae);
@ -787,7 +787,7 @@ double PairRESquared::resquared_analytic(const int i, const int j,
dUr = pbsr*(eta*dchi + deta*chi)-dh12*dspr;
ttor[i] = -(dUa*Ua+dUr*Ur);
}
// torque on j
if (!(force->newton_pair || j < atom->nlocal))
@ -829,12 +829,12 @@ double PairRESquared::resquared_analytic(const int i, const int j,
------------------------------------------------------------------------- */
double PairRESquared::resquared_lj(const int i, const int j,
const RE2Vars &wi, const double *r,
const double rsq, double *fforce,
const RE2Vars &wi, const double *r,
const double rsq, double *fforce,
double *ttor, bool calc_torque)
{
int *type = atom->type;
// pair computations for energy, force, torque
double rnorm; // L2 norm of r
@ -847,7 +847,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
double sigh; // sigma/h12
double tprod; // chi*sigh
double Ua,Ur; // attractive/repulsive parts of potential
// pair computations for force, torque
double sec; // sigma*chi
@ -863,7 +863,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
double dchi,dh12; // derivatives of chi,h12
double dUr,dUa; // derivatives of Ua,Ur
double h12p3; // h12^3
// pair computations for torque
double fwae[3]; // -fourw'*aTe
@ -943,7 +943,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
hsec = h12+3.0*sec;
dspu = 1.0/h12-1.0/hsec+stemp;
pbsu = 3.0*sigma[type[i]][type[j]]/hsec;
stemp = 1.0/(shape1[type[i]][0]*cr60+h12)+
1.0/(shape1[type[i]][1]*cr60+h12)+
1.0/(shape1[type[i]][2]*cr60+h12)+
@ -951,7 +951,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
hsec = h12+b_alpha*sec;
dspr = 7.0/h12-1.0/hsec+stemp;
pbsr = b_alpha*sigma[type[i]][type[j]]/hsec;
for (int i=0; i<3; i++) {
u[0] = -rhat[i]*rhat[0];
u[1] = -rhat[i]*rhat[1];
@ -966,7 +966,7 @@ double PairRESquared::resquared_lj(const int i, const int j,
dUr = pbsr*dchi-dh12*dspr;
fforce[i]=dUr*Ur+dUa*Ua;
}
// torque on i
if (calc_torque) {

10
src/ASPHERE/pair_resquared.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -64,7 +64,7 @@ class PairRESquared : public Pair {
double A[3][3]; // Rotation matrix (lab->body)
double aTe[3][3]; // A'*E
double gamma[3][3]; // A'*S^2*A
// per particle precomputations for torque
double sa[3][3]; // S^2*A;
@ -72,7 +72,7 @@ class PairRESquared : public Pair {
double lAtwo[3][3][3]; // A'*S^2*lA
double lAsa[3][3][3]; // lAtwo+lA'*sa
};
void allocate();
void precompute_i(const int i,RE2Vars &ws);
@ -82,8 +82,8 @@ class PairRESquared : public Pair {
const double *r, const double rsq,
double *fforce, double *ttor,
double *rtor);
double resquared_lj(const int i, const int j, const RE2Vars &wi,
const double *r, const double rsq, double *fforce,
double resquared_lj(const int i, const int j, const RE2Vars &wi,
const double *r, const double rsq, double *fforce,
double *ttor, bool calc_torque);
double cr60; // 60^1/3

446
src/ASPHERE/pair_tri_lj.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -92,12 +92,12 @@ void PairTriLJ::compute(int eflag, int vflag)
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// grow discrete list if necessary and initialize
if (nall > nmax) {
@ -130,259 +130,259 @@ void PairTriLJ::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq >= cutsq[itype][jtype]) continue;
// tri/tri interactions = NxN particles
// c1,c2,c3 = corner pts of triangle I or J
evdwl = 0.0;
if (tri[i] >= 0 && tri[j] >= 0) {
if (dnum[i] == 0) {
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
dfirst[i] = ndiscrete;
discretize(i,sigma[itype][itype],dc1,dc2,dc3);
dnum[i] = ndiscrete - dfirst[i];
}
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[i] == 0) {
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
dfirst[i] = ndiscrete;
discretize(i,sigma[itype][itype],dc1,dc2,dc3);
dnum[i] = ndiscrete - dfirst[i];
}
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[j] == 0) {
MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
dfirst[j] = ndiscrete;
discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
dnum[j] = ndiscrete - dfirst[j];
}
npj = dnum[j];
jfirst = dfirst[j];
if (dnum[j] == 0) {
MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
dfirst[j] = ndiscrete;
discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
dnum[j] = ndiscrete - dfirst[j];
}
npj = dnum[j];
jfirst = dfirst[j];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
dzi = discrete[ifirst+ni].dz;
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
dzi = discrete[ifirst+ni].dz;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
dzj = discrete[jfirst+nj].dz;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
dzj = discrete[jfirst+nj].dz;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xi[2] = x[i][2] + dzi;
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
xj[2] = x[j][2] + dzj;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xi[2] = x[i][2] + dzi;
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
xj[2] = x[j][2] + dzj;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
ti[0] = dyi*fi[2] - dzi*fi[1];
ti[1] = dzi*fi[0] - dxi*fi[2];
ti[2] = dxi*fi[1] - dyi*fi[0];
torque[i][0] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
tj[0] = dyj*fj[2] - dzj*fj[1];
tj[1] = dzj*fj[0] - dxj*fj[2];
tj[2] = dxj*fj[1] - dyj*fj[0];
torque[j][0] += tj[0];
torque[j][1] += tj[1];
torque[j][2] += tj[2];
}
}
}
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
ti[0] = dyi*fi[2] - dzi*fi[1];
ti[1] = dzi*fi[0] - dxi*fi[2];
ti[2] = dxi*fi[1] - dyi*fi[0];
torque[i][0] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
tj[0] = dyj*fj[2] - dzj*fj[1];
tj[1] = dzj*fj[0] - dxj*fj[2];
tj[2] = dxj*fj[1] - dyj*fj[0];
torque[j][0] += tj[0];
torque[j][1] += tj[1];
torque[j][2] += tj[2];
}
}
}
// tri/particle interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle I
} else if (tri[i] >= 0) {
if (dnum[i] == 0) {
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
dfirst[i] = ndiscrete;
discretize(i,sigma[itype][itype],dc1,dc2,dc3);
dnum[i] = ndiscrete - dfirst[i];
}
npi = dnum[i];
ifirst = dfirst[i];
if (dnum[i] == 0) {
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
dfirst[i] = ndiscrete;
discretize(i,sigma[itype][itype],dc1,dc2,dc3);
dnum[i] = ndiscrete - dfirst[i];
}
npi = dnum[i];
ifirst = dfirst[i];
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
dzi = discrete[ifirst+ni].dz;
for (ni = 0; ni < npi; ni++) {
dxi = discrete[ifirst+ni].dx;
dyi = discrete[ifirst+ni].dy;
dzi = discrete[ifirst+ni].dz;
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xi[2] = x[i][2] + dzi;
xj[0] = x[j][0];
xj[1] = x[j][1];
xj[2] = x[j][2];
xi[0] = x[i][0] + dxi;
xi[1] = x[i][1] + dyi;
xi[2] = x[i][2] + dzi;
xj[0] = x[j][0];
xj[1] = x[j][1];
xj[2] = x[j][2];
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
ti[0] = dyi*fi[2] - dzi*fi[1];
ti[1] = dzi*fi[0] - dxi*fi[2];
ti[2] = dxi*fi[1] - dyi*fi[0];
torque[i][2] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
}
}
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
ti[0] = dyi*fi[2] - dzi*fi[1];
ti[1] = dzi*fi[0] - dxi*fi[2];
ti[2] = dxi*fi[1] - dyi*fi[0];
torque[i][2] += ti[0];
torque[i][1] += ti[1];
torque[i][2] += ti[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
}
}
// particle/tri interaction = Nx1 particles
// c1,c2,c3 = corner pts of triangle J
} else if (tri[j] >= 0) {
if (dnum[j] == 0) {
MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
dfirst[j] = ndiscrete;
discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
dnum[j] = ndiscrete - dfirst[j];
}
npj = dnum[j];
jfirst = dfirst[j];
if (dnum[j] == 0) {
MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
dfirst[j] = ndiscrete;
discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
dnum[j] = ndiscrete - dfirst[j];
}
npj = dnum[j];
jfirst = dfirst[j];
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
dzj = discrete[jfirst+nj].dz;
for (nj = 0; nj < npj; nj++) {
dxj = discrete[jfirst+nj].dx;
dyj = discrete[jfirst+nj].dy;
dzj = discrete[jfirst+nj].dz;
xi[0] = x[i][0];
xi[1] = x[i][1];
xi[2] = x[i][2];
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
xj[2] = x[j][2] + dzj;
xi[0] = x[i][0];
xi[1] = x[i][1];
xi[2] = x[i][2];
xj[0] = x[j][0] + dxj;
xj[1] = x[j][1] + dyj;
xj[2] = x[j][2] + dzj;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
delx = xi[0] - xj[0];
dely = xi[1] - xj[1];
delz = xi[2] - xj[2];
rsq = delx*delx + dely*dely + delz*delz;
sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
sig3 = sig*sig*sig;
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
term1 = 2.0 * term2 * sig3*sig3;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (term1*r6inv - term2);
fpair = forcelj*r2inv;
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
tj[0] = dyj*fj[2] - dzj*fj[1];
tj[1] = dzj*fj[0] - dxj*fj[2];
tj[2] = dxj*fj[1] - dyj*fj[0];
torque[j][0] += tj[0];
torque[j][1] += tj[1];
torque[j][2] += tj[2];
}
}
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
fi[0] = delx*fpair;
fi[1] = dely*fpair;
fi[2] = delz*fpair;
f[i][0] += fi[0];
f[i][1] += fi[1];
f[i][2] += fi[2];
if (newton_pair || j < nlocal) {
fj[0] = -delx*fpair;
fj[1] = -dely*fpair;
fj[2] = -delz*fpair;
f[j][0] += fj[0];
f[j][1] += fj[1];
f[j][2] += fj[2];
tj[0] = dyj*fj[2] - dzj*fj[1];
tj[1] = dzj*fj[0] - dxj*fj[2];
tj[2] = dxj*fj[1] - dyj*fj[0];
torque[j][0] += tj[0];
torque[j][1] += tj[1];
torque[j][2] += tj[2];
}
}
// particle/particle interaction = 1x1 particles
} else {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = forcelj*r2inv;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = forcelj*r2inv;
if (eflag)
evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (eflag)
evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
evdwl,0.0,fpair,delx,dely,delz);
}
}
@ -390,7 +390,7 @@ void PairTriLJ::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairTriLJ::allocate()
@ -415,7 +415,7 @@ void PairTriLJ::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairTriLJ::settings(int narg, char **arg)
@ -430,7 +430,7 @@ void PairTriLJ::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@ -440,7 +440,7 @@ void PairTriLJ::settings(int narg, char **arg)
void PairTriLJ::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 5)
if (narg < 4 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@ -476,7 +476,7 @@ double PairTriLJ::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@ -504,7 +504,7 @@ double PairTriLJ::init_one(int i, int j)
------------------------------------------------------------------------- */
void PairTriLJ::discretize(int i, double sigma,
double *c1, double *c2, double *c3)
double *c1, double *c2, double *c3)
{
double c1c2[3],c2c3[3],c1c3[3];
@ -529,7 +529,7 @@ void PairTriLJ::discretize(int i, double sigma,
if (ndiscrete == dmax) {
dmax += DELTA;
discrete = (Discrete *)
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
}
discrete[ndiscrete].dx = centroid[0];
discrete[ndiscrete].dy = centroid[1];
@ -582,7 +582,7 @@ void PairTriLJ::discretize(int i, double sigma,
/*
void PairTriLJ::discretize(int i, double sigma,
double *c1, double *c2, double *c3)
double *c1, double *c2, double *c3)
{
double centroid[3],dc1[3],dc2[3],dc3[3];
@ -605,7 +605,7 @@ void PairTriLJ::discretize(int i, double sigma,
if (ndiscrete == dmax) {
dmax += DELTA;
discrete = (Discrete *)
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
}
discrete[ndiscrete].dx = centroid[0];
discrete[ndiscrete].dy = centroid[1];

2
src/ASPHERE/pair_tri_lj.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

28
src/CLASS2/angle_class2.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -116,10 +116,10 @@ void AngleClass2::compute(int eflag, int vflag)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@ -131,14 +131,14 @@ void AngleClass2::compute(int eflag, int vflag)
dtheta3 = dtheta2*dtheta;
dtheta4 = dtheta3*dtheta;
de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
de_angle = 2.0*k2[type]*dtheta + 3.0*k3[type]*dtheta2 +
4.0*k4[type]*dtheta3;
a = -de_angle*s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
f1[0] = a11*delx1 + a12*delx2;
f1[1] = a11*dely1 + a12*dely2;
f1[2] = a11*delz1 + a12*delz2;
@ -227,7 +227,7 @@ void AngleClass2::compute(int eflag, int vflag)
}
if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
delx1,dely1,delz1,delx2,dely2,delz2);
delx1,dely1,delz1,delx2,dely2,delz2);
}
}
@ -283,7 +283,7 @@ void AngleClass2::coeff(int narg, char **arg)
double bb_k_one = force->numeric(arg[2]);
double bb_r1_one = force->numeric(arg[3]);
double bb_r2_one = force->numeric(arg[4]);
for (int i = ilo; i <= ihi; i++) {
bb_k[i] = bb_k_one;
bb_r1[i] = bb_r1_one;
@ -299,7 +299,7 @@ void AngleClass2::coeff(int narg, char **arg)
double ba_k2_one = force->numeric(arg[3]);
double ba_r1_one = force->numeric(arg[4]);
double ba_r2_one = force->numeric(arg[5]);
for (int i = ilo; i <= ihi; i++) {
ba_k1[i] = ba_k1_one;
ba_k2[i] = ba_k2_one;
@ -316,7 +316,7 @@ void AngleClass2::coeff(int narg, char **arg)
double k2_one = force->numeric(arg[2]);
double k3_one = force->numeric(arg[3]);
double k4_one = force->numeric(arg[4]);
// convert theta0 from degrees to radians
for (int i = ilo; i <= ihi; i++) {
@ -365,7 +365,7 @@ void AngleClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleClass2::read_restart(FILE *fp)
@ -381,7 +381,7 @@ void AngleClass2::read_restart(FILE *fp)
fread(&bb_k[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r1[1],sizeof(double),atom->nangletypes,fp);
fread(&bb_r2[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_k1[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_k2[1],sizeof(double),atom->nangletypes,fp);
fread(&ba_r1[1],sizeof(double),atom->nangletypes,fp);
@ -427,7 +427,7 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
@ -436,9 +436,9 @@ double AngleClass2::single(int type, int i1, int i2, int i3)
double dtheta2 = dtheta*dtheta;
double dtheta3 = dtheta2*dtheta;
double dtheta4 = dtheta3*dtheta;
double energy = k2[type]*dtheta2 + k3[type]*dtheta3 + k4[type]*dtheta4;
double dr1 = r1 - bb_r1[type];
double dr2 = r2 - bb_r2[type];
energy += bb_k[type]*dr1*dr2;

2
src/CLASS2/angle_class2.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

10
src/CLASS2/bond_class2.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -124,7 +124,7 @@ void BondClass2::allocate()
}
/* ----------------------------------------------------------------------
set coeffs from one line in input script or data file
set coeffs from one line in input script or data file
------------------------------------------------------------------------- */
void BondClass2::coeff(int narg, char **arg)
@ -154,7 +154,7 @@ void BondClass2::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
return an equilbrium bond length
return an equilbrium bond length
------------------------------------------------------------------------- */
double BondClass2::equilibrium_distance(int i)
@ -163,7 +163,7 @@ double BondClass2::equilibrium_distance(int i)
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void BondClass2::write_restart(FILE *fp)
@ -175,7 +175,7 @@ void BondClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void BondClass2::read_restart(FILE *fp)

2
src/CLASS2/bond_class2.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

152
src/CLASS2/dihedral_class2.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -181,19 +181,19 @@ void DihedralClass2::compute(int eflag, int vflag)
costh12 = (vb1x*vb2x + vb1y*vb2y + vb1z*vb2z) * r12c1;
costh13 = c0;
costh23 = (vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z) * r12c2;
// cos and sin of 2 angles and final c
sin2 = MAX(1.0 - costh12*costh12,0.0);
sc1 = sqrt(sin2);
if (sc1 < SMALL) sc1 = SMALL;
sc1 = 1.0/sc1;
sin2 = MAX(1.0 - costh23*costh23,0.0);
sc2 = sqrt(sin2);
if (sc2 < SMALL) sc2 = SMALL;
sc2 = 1.0/sc2;
s1 = sc1 * sc1;
s2 = sc2 * sc2;
s12 = sc1 * sc2;
@ -205,19 +205,19 @@ void DihedralClass2::compute(int eflag, int vflag)
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
char str[128];
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
@ -235,7 +235,7 @@ void DihedralClass2::compute(int eflag, int vflag)
a12 = r12c1 * (costh12*c*s1 + costh23*s12);
a13 = rb1*rb3*s12;
a23 = r12c2 * (-costh23*c*s2 - costh12*s12);
sx1 = a11*vb1x + a12*vb2x + a13*vb3x;
sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
sx12 = a13*vb1x + a23*vb2x + a33*vb3x;
@ -263,18 +263,18 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
dphidr[i][j] = -dcosphidr[i][j] / sinphi;
dphidr[i][j] = -dcosphidr[i][j] / sinphi;
// energy
dphi1 = phi - phi1[type];
dphi2 = 2.0*phi - phi2[type];
dphi3 = 3.0*phi - phi3[type];
if (eflag) edihedral = k1[type]*(1.0 - cos(dphi1)) +
k2[type]*(1.0 - cos(dphi2)) +
k3[type]*(1.0 - cos(dphi3));
k2[type]*(1.0 - cos(dphi2)) +
k3[type]*(1.0 - cos(dphi3));
de_dihedral = k1[type]*sin(dphi1) + 2.0*k2[type]*sin(dphi2) +
3.0*k3[type]*sin(dphi3);
@ -282,18 +282,18 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = de_dihedral*dphidr[i][j];
fabcd[i][j] = de_dihedral*dphidr[i][j];
// set up d(bond)/d(r) array
// dbonddr(i,j,k) = bond i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dbonddr[i][j][k] = 0.0;
for (k = 0; k < 3; k++)
dbonddr[i][j][k] = 0.0;
// bond1
dbonddr[0][0][0] = vb1x / r1;
dbonddr[0][0][1] = vb1y / r1;
dbonddr[0][0][2] = vb1z / r1;
@ -311,7 +311,7 @@ void DihedralClass2::compute(int eflag, int vflag)
dbonddr[1][2][2] = -vb2z / r2;
// bond3
dbonddr[2][2][0] = vb3x / r3;
dbonddr[2][2][1] = vb3y / r3;
dbonddr[2][2][2] = vb3z / r3;
@ -324,71 +324,71 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 2; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
t1 = costh12 / r1mag2;
t2 = costh23 / r2mag2;
t3 = costh12 / r2mag2;
t4 = costh23 / r3mag2;
// angle12
dthetadr[0][0][0] = sc1 * ((t1 * vb1x) - (vb2x * r12c1));
dthetadr[0][0][1] = sc1 * ((t1 * vb1y) - (vb2y * r12c1));
dthetadr[0][0][2] = sc1 * ((t1 * vb1z) - (vb2z * r12c1));
dthetadr[0][1][0] = sc1 * ((-t1 * vb1x) + (vb2x * r12c1) +
(-t3 * vb2x) + (vb1x * r12c1));
(-t3 * vb2x) + (vb1x * r12c1));
dthetadr[0][1][1] = sc1 * ((-t1 * vb1y) + (vb2y * r12c1) +
(-t3 * vb2y) + (vb1y * r12c1));
(-t3 * vb2y) + (vb1y * r12c1));
dthetadr[0][1][2] = sc1 * ((-t1 * vb1z) + (vb2z * r12c1) +
(-t3 * vb2z) + (vb1z * r12c1));
dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
(-t3 * vb2z) + (vb1z * r12c1));
dthetadr[0][2][0] = sc1 * ((t3 * vb2x) - (vb1x * r12c1));
dthetadr[0][2][1] = sc1 * ((t3 * vb2y) - (vb1y * r12c1));
dthetadr[0][2][2] = sc1 * ((t3 * vb2z) - (vb1z * r12c1));
// angle23
dthetadr[1][1][0] = sc2 * ((t2 * vb2x) + (vb3x * r12c2));
dthetadr[1][1][1] = sc2 * ((t2 * vb2y) + (vb3y * r12c2));
dthetadr[1][1][2] = sc2 * ((t2 * vb2z) + (vb3z * r12c2));
dthetadr[1][2][0] = sc2 * ((-t2 * vb2x) - (vb3x * r12c2) +
(t4 * vb3x) + (vb2x * r12c2));
(t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][2][1] = sc2 * ((-t2 * vb2y) - (vb3y * r12c2) +
(t4 * vb3y) + (vb2y * r12c2));
(t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][2][2] = sc2 * ((-t2 * vb2z) - (vb3z * r12c2) +
(t4 * vb3z) + (vb2z * r12c2));
(t4 * vb3z) + (vb2z * r12c2));
dthetadr[1][3][0] = -sc2 * ((t4 * vb3x) + (vb2x * r12c2));
dthetadr[1][3][1] = -sc2 * ((t4 * vb3y) + (vb2y * r12c2));
dthetadr[1][3][2] = -sc2 * ((t4 * vb3z) + (vb2z * r12c2));
// mid-bond/torsion coupling
// energy on bond2 (middle bond)
cos2phi = cos(2.0*phi);
cos3phi = cos(3.0*phi);
bt1 = mbt_f1[type] * cosphi;
bt2 = mbt_f2[type] * cos2phi;
bt3 = mbt_f3[type] * cos3phi;
sumbte = bt1 + bt2 + bt3;
db = r2 - mbt_r0[type];
if (eflag) edihedral += db * sumbte;
// force on bond2
bt1 = -mbt_f1[type] * sinphi;
bt2 = -2.0 * mbt_f2[type] * sin(2.0*phi);
bt3 = -3.0 * mbt_f3[type] * sin(3.0*phi);
sumbtf = bt1 + bt2 + bt3;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[1][i][j];
// end-bond/torsion coupling
// energy on bond1 (first bond)
@ -410,7 +410,7 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
fabcd[i][j] -= db*sumbtf*dphidr[i][j] + sumbte*dbonddr[0][i][j];
// end-bond/torsion coupling
// energy on bond3 (last bond)
@ -432,7 +432,7 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
fabcd[i][j] += db*sumbtf*dphidr[i][j] + sumbte*dbonddr[2][i][j];
// angle/torsion coupling
// energy on angle1
@ -454,7 +454,7 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
fabcd[i][j] -= da*sumbtf*dphidr[i][j] + sumbte*dthetadr[0][i][j];
// energy on angle2
@ -475,20 +475,20 @@ void DihedralClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
fabcd[i][j] += da*sumbtf*dphidr[i][j] + sumbte*dthetadr[1][i][j];
// angle/angle/torsion coupling
da1 = acos(costh12) - aat_theta0_1[type];
da2 = acos(costh23) - aat_theta0_2[type];
if (eflag) edihedral += aat_k[type]*da1*da2*cosphi;
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] -= aat_k[type] *
(cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
sinphi * da1*da2*dphidr[i][j]);
fabcd[i][j] -= aat_k[type] *
(cosphi * (da2*dthetadr[0][i][j] - da1*dthetadr[1][i][j]) +
sinphi * da1*da2*dphidr[i][j]);
// bond1/bond3 coupling
@ -502,7 +502,7 @@ void DihedralClass2::compute(int eflag, int vflag)
tk2 = -bb13t_k[type] * dr2 / r1;
if (eflag) edihedral += bb13t_k[type]*dr1*dr2;
fabcd[0][0] += tk2 * vb1x;
fabcd[0][1] += tk2 * vb1y;
fabcd[0][2] += tk2 * vb1z;
@ -510,7 +510,7 @@ void DihedralClass2::compute(int eflag, int vflag)
fabcd[1][0] -= tk2 * vb1x;
fabcd[1][1] -= tk2 * vb1y;
fabcd[1][2] -= tk2 * vb1z;
fabcd[2][0] -= tk1 * vb3x;
fabcd[2][1] -= tk1 * vb3y;
fabcd[2][2] -= tk1 * vb3z;
@ -548,8 +548,8 @@ void DihedralClass2::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,
fabcd[0],fabcd[2],fabcd[3],
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
fabcd[0],fabcd[2],fabcd[3],
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
@ -608,7 +608,7 @@ void DihedralClass2::allocate()
memory->create(setflag_aat,n+1,"dihedral:setflag_aat");
memory->create(setflag_bb13t,n+1,"dihedral:setflag_bb13t");
for (int i = 1; i <= n; i++)
setflag[i] = setflag_d[i] = setflag_mbt[i] = setflag_ebt[i] =
setflag[i] = setflag_d[i] = setflag_mbt[i] = setflag_ebt[i] =
setflag_at[i] = setflag_aat[i] = setflag_bb13t[i] = 0;
}
@ -639,7 +639,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double f2_one = force->numeric(arg[3]);
double f3_one = force->numeric(arg[4]);
double r0_one = force->numeric(arg[5]);
for (int i = ilo; i <= ihi; i++) {
mbt_f1[i] = f1_one;
mbt_f2[i] = f2_one;
@ -660,7 +660,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double f3_2_one = force->numeric(arg[7]);
double r0_1_one = force->numeric(arg[8]);
double r0_2_one = force->numeric(arg[9]);
for (int i = ilo; i <= ihi; i++) {
ebt_f1_1[i] = f1_1_one;
ebt_f2_1[i] = f2_1_one;
@ -687,7 +687,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double theta0_2_one = force->numeric(arg[9]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
at_f1_1[i] = f1_1_one;
at_f2_1[i] = f2_1_one;
@ -709,7 +709,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double theta0_2_one = force->numeric(arg[4]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
aat_k[i] = k_one;
aat_theta0_1[i] = theta0_1_one/180.0 * MY_PI;
@ -724,7 +724,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double k_one = force->numeric(arg[2]);
double r10_one = force->numeric(arg[3]);
double r30_one = force->numeric(arg[4]);
for (int i = ilo; i <= ihi; i++) {
bb13t_k[i] = k_one;
bb13t_r10[i] = r10_one;
@ -742,7 +742,7 @@ void DihedralClass2::coeff(int narg, char **arg)
double phi2_one = force->numeric(arg[4]);
double k3_one = force->numeric(arg[5]);
double phi3_one = force->numeric(arg[6]);
// convert phi's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
@ -761,12 +761,12 @@ void DihedralClass2::coeff(int narg, char **arg)
for (int i = ilo; i <= ihi; i++)
if (setflag_d[i] == 1 && setflag_mbt[i] == 1 && setflag_ebt[i] == 1 &&
setflag_at[i] == 1 && setflag_aat[i] == 1 && setflag_bb13t[i] == 1)
setflag_at[i] == 1 && setflag_aat[i] == 1 && setflag_bb13t[i] == 1)
setflag[i] = 1;
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralClass2::write_restart(FILE *fp)
@ -813,7 +813,7 @@ void DihedralClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralClass2::read_restart(FILE *fp)

2
src/CLASS2/dihedral_class2.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

360
src/CLASS2/improper_class2.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -91,10 +91,10 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
dthetadr[i][j][k] = 0.0;
drAB[i][j][k] = 0.0;
drCB[i][j][k] = 0.0;
drDB[i][j][k] = 0.0;
dthetadr[i][j][k] = 0.0;
drAB[i][j][k] = 0.0;
drCB[i][j][k] = 0.0;
drDB[i][j][k] = 0.0;
}
double **x = atom->x;
@ -133,43 +133,43 @@ void ImproperClass2::compute(int eflag, int vflag)
// bond lengths and associated values
for (i = 0; i < 3; i++) {
rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
delr[i][2]*delr[i][2];
rmag2[i] = delr[i][0]*delr[i][0] + delr[i][1]*delr[i][1] +
delr[i][2]*delr[i][2];
rmag[i] = sqrt(rmag2[i]);
rinvmag[i] = 1.0/rmag[i];
}
// angle ABC, CBD, ABD
costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
costheta[0] = (delr[0][0]*delr[1][0] + delr[0][1]*delr[1][1] +
delr[0][2]*delr[1][2]) / (rmag[0]*rmag[1]);
costheta[1] = (delr[1][0]*delr[2][0] + delr[1][1]*delr[2][1] +
delr[1][2]*delr[2][2]) / (rmag[1]*rmag[2]);
costheta[2] = (delr[0][0]*delr[2][0] + delr[0][1]*delr[2][1] +
delr[0][2]*delr[2][2]) / (rmag[0]*rmag[2]);
// angle error check
for (i = 0; i < 3; i++) {
if (costheta[i] == -1.0) {
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,
"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
int me;
MPI_Comm_rank(world,&me);
if (screen) {
char str[128];
sprintf(str,
"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
me,update->ntimestep,
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
error->warning(FLERR,str,0);
fprintf(screen," 1st atom: %d %g %g %g\n",
me,x[i1][0],x[i1][1],x[i1][2]);
fprintf(screen," 2nd atom: %d %g %g %g\n",
me,x[i2][0],x[i2][1],x[i2][2]);
fprintf(screen," 3rd atom: %d %g %g %g\n",
me,x[i3][0],x[i3][1],x[i3][2]);
fprintf(screen," 4th atom: %d %g %g %g\n",
me,x[i4][0],x[i4][1],x[i4][2]);
}
}
}
@ -223,7 +223,7 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
ddelr[i][j] = 0.0;
ddelr[i][j] = 0.0;
ddelr[0][0] = 1.0;
ddelr[0][1] = -1.0;
@ -238,19 +238,19 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++) {
dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
}
for (k = 0; k < 3; k++) {
dr[i][j][k] = delr[i][k] * ddelr[i][j] / rmag[i];
dinvr[i][j][k] = -dr[i][j][k] / rmag2[i];
}
// compute d(1 / (|r_AB| * |r_CB| * |r_DB|) / dr
// i = atom A/B/C/D, j = X/Y/Z
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
rinvmag[0] * dinvr[2][i][j]) +
rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
dinv3r[i][j] = rinvmag[1] * (rinvmag[2] * dinvr[0][i][j] +
rinvmag[0] * dinvr[2][i][j]) +
rinvmag[2] * rinvmag[0] * dinvr[1][i][j];
// compute d(theta)/d(r) for 3 angles
// angleABC
@ -259,30 +259,30 @@ void ImproperClass2::compute(int eflag, int vflag)
tt3 = costheta[0] / rmag2[1];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[0]);
dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[1][0] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[1][1] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[1][2] * rinvmag[0] * rinvmag[1]) +
(tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][0] = sc1 * ((tt3 * delr[1][0]) -
(delr[0][0] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][1] = sc1 * ((tt3 * delr[1][1]) -
(delr[0][1] * rinvmag[0] * rinvmag[1]));
dthetadr[0][2][2] = sc1 * ((tt3 * delr[1][2]) -
(delr[0][2] * rinvmag[0] * rinvmag[1]));
// angleCBD
@ -290,30 +290,30 @@ void ImproperClass2::compute(int eflag, int vflag)
tt3 = costheta[1] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[1]);
dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]));
dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
dthetadr[1][2][0] = sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][1] = sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]));
dthetadr[1][2][2] = sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]));
dthetadr[1][1][0] = -sc1 * ((tt1 * delr[1][0]) -
(delr[2][0] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][1] = -sc1 * ((tt1 * delr[1][1]) -
(delr[2][1] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][1][2] = -sc1 * ((tt1 * delr[1][2]) -
(delr[2][2] * rinvmag[1] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[1][0] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[1][1] * rinvmag[2] * rinvmag[1]));
dthetadr[1][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[1][2] * rinvmag[2] * rinvmag[1]));
// angleABD
@ -321,30 +321,30 @@ void ImproperClass2::compute(int eflag, int vflag)
tt3 = costheta[2] / rmag2[2];
sc1 = 1.0 / sqrt(1.0 - cossqtheta[2]);
dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]));
dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
dthetadr[2][0][0] = sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][1] = sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]));
dthetadr[2][0][2] = sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]));
dthetadr[2][1][0] = -sc1 * ((tt1 * delr[0][0]) -
(delr[2][0] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][1] = -sc1 * ((tt1 * delr[0][1]) -
(delr[2][1] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][1][2] = -sc1 * ((tt1 * delr[0][2]) -
(delr[2][2] * rinvmag[0] * rinvmag[2]) +
(tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][0] = sc1 * ((tt3 * delr[2][0]) -
(delr[0][0] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][1] = sc1 * ((tt3 * delr[2][1]) -
(delr[0][1] * rinvmag[2] * rinvmag[0]));
dthetadr[2][3][2] = sc1 * ((tt3 * delr[2][2]) -
(delr[0][2] * rinvmag[2] * rinvmag[0]));
// compute d( 1 / sin(theta))/dr
// i = angle, j = atom, k = direction
@ -352,8 +352,8 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++) {
cossin2 = -costheta[i] / sinsqtheta[i];
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
for (k = 0; k < 3; k++)
dinvsth[i][j][k] = cossin2 * dthetadr[i][j][k];
}
// compute d(1 / sin(theta) * |r_AB| * |r_CB| * |r_DB|)/dr
@ -361,12 +361,12 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
(inv3r * dinvsth[1][i][j]);
dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
(inv3r * dinvsth[2][i][j]);
dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
(inv3r * dinvsth[0][i][j]);
dinvs3r[0][i][j] = (invstheta[1] * dinv3r[i][j]) +
(inv3r * dinvsth[1][i][j]);
dinvs3r[1][i][j] = (invstheta[2] * dinv3r[i][j]) +
(inv3r * dinvsth[2][i][j]);
dinvs3r[2][i][j] = (invstheta[0] * dinv3r[i][j]) +
(inv3r * dinvsth[0][i][j]);
}
// drCB(i,j,k), etc
@ -390,12 +390,12 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[1],drDB[i][j],rCBxdrDB);
cross(drCB[i][j],delr[2],drCBxrDB);
for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
dot1 = dot(dd,delr[0]);
dot2 = dot(rCBxrDB,drAB[i][j]);
fdot[0][j][i] = dot1 + dot2;
cross(delr[1],drDB[i][j],rCBxdrDB);
cross(drCB[i][j],delr[2],drCBxrDB);
for (k = 0; k < 3; k++) dd[k] = rCBxdrDB[k] + drCBxrDB[k];
dot1 = dot(dd,delr[0]);
dot2 = dot(rCBxrDB,drAB[i][j]);
fdot[0][j][i] = dot1 + dot2;
}
// d((r_DB x r_AB) dot r_CB)
@ -407,12 +407,12 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[2],drAB[i][j],rDBxdrAB);
cross(drDB[i][j],delr[0],drDBxrAB);
for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
dot1 = dot(dd,delr[1]);
dot2 = dot(rDBxrAB,drCB[i][j]);
fdot[1][j][i] = dot1 + dot2;
cross(delr[2],drAB[i][j],rDBxdrAB);
cross(drDB[i][j],delr[0],drDBxrAB);
for (k = 0; k < 3; k++) dd[k] = rDBxdrAB[k] + drDBxrAB[k];
dot1 = dot(dd,delr[1]);
dot2 = dot(rDBxrAB,drCB[i][j]);
fdot[1][j][i] = dot1 + dot2;
}
// d((r_AB x r_CB) dot r_DB)
@ -424,33 +424,33 @@ void ImproperClass2::compute(int eflag, int vflag)
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++) {
cross(delr[0],drCB[i][j],rABxdrCB);
cross(drAB[i][j],delr[1],drABxrCB);
for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
dot1 = dot(dd,delr[2]);
dot2 = dot(rABxrCB,drDB[i][j]);
fdot[2][j][i] = dot1 + dot2;
cross(delr[0],drCB[i][j],rABxdrCB);
cross(drAB[i][j],delr[1],drABxrCB);
for (k = 0; k < 3; k++) dd[k] = rABxdrCB[k] + drABxrCB[k];
dot1 = dot(dd,delr[2]);
dot2 = dot(rABxrCB,drDB[i][j]);
fdot[2][j][i] = dot1 + dot2;
}
// force on each atom
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++) {
ftmp = (fdot[0][i][j] * invs3r[0]) +
(dinvs3r[0][i][j] * dotCBDBAB);
dchi[0][i][j] = ftmp / cos(chiABCD);
ftmp = (fdot[1][i][j] * invs3r[1]) +
(dinvs3r[1][i][j] * dotDBABCB);
dchi[1][i][j] = ftmp / cos(chiCBDA);
ftmp = (fdot[2][i][j] * invs3r[2]) +
(dinvs3r[2][i][j] * dotABCBDB);
dchi[2][i][j] = ftmp / cos(chiDBAC);
dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
ftmp = (fdot[0][i][j] * invs3r[0]) +
(dinvs3r[0][i][j] * dotCBDBAB);
dchi[0][i][j] = ftmp / cos(chiABCD);
ftmp = (fdot[1][i][j] * invs3r[1]) +
(dinvs3r[1][i][j] * dotDBABCB);
dchi[1][i][j] = ftmp / cos(chiCBDA);
ftmp = (fdot[2][i][j] * invs3r[2]) +
(dinvs3r[2][i][j] * dotABCBDB);
dchi[2][i][j] = ftmp / cos(chiDBAC);
dtotalchi[i][j] = (dchi[0][i][j]+dchi[1][i][j]+dchi[2][i][j]) / 3.0;
}
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
fabcd[i][j] = -2.0*k0[type] * deltachi*dtotalchi[i][j];
// apply force to each of 4 atoms
@ -480,11 +480,11 @@ void ImproperClass2::compute(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,
fabcd[0],fabcd[2],fabcd[3],
delr[0][0],delr[0][1],delr[0][2],
delr[1][0],delr[1][1],delr[1][2],
delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
delr[2][2]-delr[1][2]);
fabcd[0],fabcd[2],fabcd[3],
delr[0][0],delr[0][1],delr[0][2],
delr[1][0],delr[1][1],delr[1][2],
delr[2][0]-delr[1][0],delr[2][1]-delr[1][1],
delr[2][2]-delr[1][2]);
}
// compute angle-angle interactions
@ -541,7 +541,7 @@ void ImproperClass2::coeff(int narg, char **arg)
double theta0_1_one = force->numeric(arg[5]);
double theta0_2_one = force->numeric(arg[6]);
double theta0_3_one = force->numeric(arg[7]);
// convert theta0's from degrees to radians
for (int i = ilo; i <= ihi; i++) {
@ -578,7 +578,7 @@ void ImproperClass2::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void ImproperClass2::write_restart(FILE *fp)
@ -595,7 +595,7 @@ void ImproperClass2::write_restart(FILE *fp)
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void ImproperClass2::read_restart(FILE *fp)
@ -681,7 +681,7 @@ void ImproperClass2::angleangle(int eflag, int vflag)
rBC = sqrt(rBCmag2);
rBDmag2 = delxBD*delxBD + delyBD*delyBD + delzBD*delzBD;
rBD = sqrt(rBDmag2);
// angle ABC, ABD, CBD
costhABC = (delxAB*delxBC + delyAB*delyBC + delzAB*delzBC) / (rAB * rBC);
@ -705,17 +705,17 @@ void ImproperClass2::angleangle(int eflag, int vflag)
// energy
if (eflag) eimproper = aa_k2[type] * dthABC * dthABD +
aa_k1[type] * dthABC * dthCBD +
aa_k3[type] * dthABD * dthCBD;
if (eflag) eimproper = aa_k2[type] * dthABC * dthABD +
aa_k1[type] * dthABC * dthCBD +
aa_k3[type] * dthABD * dthCBD;
// d(theta)/d(r) array
// angle i, atom j, coordinate k
for (i = 0; i < 3; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
for (k = 0; k < 3; k++)
dthetadr[i][j][k] = 0.0;
// angle ABC
@ -728,11 +728,11 @@ void ImproperClass2::angleangle(int eflag, int vflag)
dthetadr[0][0][1] = sc1 * ((t1 * delyAB) - (delyBC * r12));
dthetadr[0][0][2] = sc1 * ((t1 * delzAB) - (delzBC * r12));
dthetadr[0][1][0] = sc1 * ((-t1 * delxAB) + (delxBC * r12) +
(-t3 * delxBC) + (delxAB * r12));
(-t3 * delxBC) + (delxAB * r12));
dthetadr[0][1][1] = sc1 * ((-t1 * delyAB) + (delyBC * r12) +
(-t3 * delyBC) + (delyAB * r12));
(-t3 * delyBC) + (delyAB * r12));
dthetadr[0][1][2] = sc1 * ((-t1 * delzAB) + (delzBC * r12) +
(-t3 * delzBC) + (delzAB * r12));
(-t3 * delzBC) + (delzAB * r12));
dthetadr[0][2][0] = sc1 * ((t3 * delxBC) - (delxAB * r12));
dthetadr[0][2][1] = sc1 * ((t3 * delyBC) - (delyAB * r12));
dthetadr[0][2][2] = sc1 * ((t3 * delzBC) - (delzAB * r12));
@ -748,11 +748,11 @@ void ImproperClass2::angleangle(int eflag, int vflag)
dthetadr[1][2][1] = sc1 * ((t1 * delyBC) - (delyBD * r12));
dthetadr[1][2][2] = sc1 * ((t1 * delzBC) - (delzBD * r12));
dthetadr[1][1][0] = sc1 * ((-t1 * delxBC) + (delxBD * r12) +
(-t3 * delxBD) + (delxBC * r12));
(-t3 * delxBD) + (delxBC * r12));
dthetadr[1][1][1] = sc1 * ((-t1 * delyBC) + (delyBD * r12) +
(-t3 * delyBD) + (delyBC * r12));
(-t3 * delyBD) + (delyBC * r12));
dthetadr[1][1][2] = sc1 * ((-t1 * delzBC) + (delzBD * r12) +
(-t3 * delzBD) + (delzBC * r12));
(-t3 * delzBD) + (delzBC * r12));
dthetadr[1][3][0] = sc1 * ((t3 * delxBD) - (delxBC * r12));
dthetadr[1][3][1] = sc1 * ((t3 * delyBD) - (delyBC * r12));
dthetadr[1][3][2] = sc1 * ((t3 * delzBD) - (delzBC * r12));
@ -768,11 +768,11 @@ void ImproperClass2::angleangle(int eflag, int vflag)
dthetadr[2][0][1] = sc1 * ((t1 * delyAB) - (delyBD * r12));
dthetadr[2][0][2] = sc1 * ((t1 * delzAB) - (delzBD * r12));
dthetadr[2][1][0] = sc1 * ((-t1 * delxAB) + (delxBD * r12) +
(-t3 * delxBD) + (delxAB * r12));
(-t3 * delxBD) + (delxAB * r12));
dthetadr[2][1][1] = sc1 * ((-t1 * delyAB) + (delyBD * r12) +
(-t3 * delyBD) + (delyAB * r12));
(-t3 * delyBD) + (delyAB * r12));
dthetadr[2][1][2] = sc1 * ((-t1 * delzAB) + (delzBD * r12) +
(-t3 * delzBD) + (delzAB * r12));
(-t3 * delzBD) + (delzAB * r12));
dthetadr[2][3][0] = sc1 * ((t3 * delxBD) - (delxAB * r12));
dthetadr[2][3][1] = sc1 * ((t3 * delyBD) - (delyAB * r12));
dthetadr[2][3][2] = sc1 * ((t3 * delzBD) - (delzAB * r12));
@ -781,13 +781,13 @@ void ImproperClass2::angleangle(int eflag, int vflag)
for (i = 0; i < 4; i++)
for (j = 0; j < 3; j++)
fabcd[i][j] = -
((aa_k1[type] *
(dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
(aa_k2[type] *
(dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
(aa_k3[type] *
(dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
fabcd[i][j] = -
((aa_k1[type] *
(dthABC*dthetadr[1][i][j] + dthCBD*dthetadr[0][i][j])) +
(aa_k2[type] *
(dthABC*dthetadr[2][i][j] + dthABD*dthetadr[0][i][j])) +
(aa_k3[type] *
(dthABD*dthetadr[1][i][j] + dthCBD*dthetadr[2][i][j])));
// apply force to each of 4 atoms
@ -817,8 +817,8 @@ void ImproperClass2::angleangle(int eflag, int vflag)
if (evflag)
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,
fabcd[0],fabcd[2],fabcd[3],
delxAB,delyAB,delzAB,delxBC,delyBC,delzBC,delxBD,delyBD,delzBD);
fabcd[0],fabcd[2],fabcd[3],
delxAB,delyAB,delzAB,delxBC,delyBC,delzBC,delxBD,delyBD,delzBD);
}
}

2
src/CLASS2/improper_class2.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

90
src/CLASS2/pair_lj_class2.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -73,7 +73,7 @@ void PairLJClass2::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -97,30 +97,30 @@ void PairLJClass2::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@ -129,7 +129,7 @@ void PairLJClass2::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2::allocate()
@ -155,7 +155,7 @@ void PairLJClass2::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairLJClass2::settings(int narg, char **arg)
@ -170,7 +170,7 @@ void PairLJClass2::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@ -218,9 +218,9 @@ double PairLJClass2::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
sigma[i][j] =
sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
@ -255,22 +255,22 @@ double PairLJClass2::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut[i][j]*cut[i][j]*cut[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
}
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2::write_restart(FILE *fp)
@ -282,9 +282,9 @@ void PairLJClass2::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@ -305,14 +305,14 @@ void PairLJClass2::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -348,8 +348,8 @@ void PairLJClass2::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJClass2::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcelj,philj;

2
src/CLASS2/pair_lj_class2.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

124
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -81,7 +81,7 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -107,43 +107,43 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@ -152,7 +152,7 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::allocate()
@ -181,7 +181,7 @@ void PairLJClass2CoulCut::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::settings(int narg, char **arg)
@ -198,10 +198,10 @@ void PairLJClass2CoulCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
@ -264,9 +264,9 @@ double PairLJClass2CoulCut::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
sigma[i][j] =
sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
@ -308,22 +308,22 @@ double PairLJClass2CoulCut::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
}
}
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2CoulCut::write_restart(FILE *fp)
@ -335,10 +335,10 @@ void PairLJClass2CoulCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@ -359,16 +359,16 @@ void PairLJClass2CoulCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -406,9 +406,9 @@ void PairLJClass2CoulCut::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJClass2CoulCut::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r3inv,r6inv,forcecoul,forcelj,phicoul,philj;

2
src/CLASS2/pair_lj_class2_coul_cut.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

130
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -90,7 +90,7 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -116,51 +116,51 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
@ -169,7 +169,7 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::allocate()
@ -196,7 +196,7 @@ void PairLJClass2CoulLong::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::settings(int narg, char **arg)
@ -213,7 +213,7 @@ void PairLJClass2CoulLong::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
}
}
@ -265,7 +265,7 @@ void PairLJClass2CoulLong::init_style()
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
if (force->kspace == NULL)
error->all(FLERR,"Pair style is incompatible with KSpace style");
g_ewald = force->kspace->g_ewald;
}
@ -281,9 +281,9 @@ double PairLJClass2CoulLong::init_one(int i, int j)
if (setflag[i][j] == 0) {
epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) *
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) /
(pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0));
sigma[i][j] =
sigma[i][j] =
pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
}
@ -322,22 +322,22 @@ double PairLJClass2CoulLong::init_one(int i, int j)
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j];
double sig6 = sig3*sig3;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
etail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 3.0*rc3) / (3.0*rc6);
ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
ptail_ij = 2.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig3 - 2.0*rc3) / rc6;
}
}
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJClass2CoulLong::write_restart(FILE *fp)
@ -349,9 +349,9 @@ void PairLJClass2CoulLong::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
@ -372,14 +372,14 @@ void PairLJClass2CoulLong::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -417,9 +417,9 @@ void PairLJClass2CoulLong::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,r3inv,r6inv,grij,expm2,t,erfc,prefactor;
double forcecoul,forcelj,phicoul,philj;

2
src/CLASS2/pair_lj_class2_coul_long.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

28
src/COLLOID/fix_wall_colloid.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -29,14 +29,14 @@ using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixWallColloid::init()
{
if (!atom->sphere_flag)
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/colloid requires atom style sphere");
// insure all particles in group are extended particles
@ -101,8 +101,8 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
if (delta >= cutoff[m]) continue;
rad = radius[i];
if (rad >= delta) {
onflag = 1;
continue;
onflag = 1;
continue;
}
new_coeff2 = coeff2[m]*rad*rad*rad;
@ -116,9 +116,9 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
r4inv = r2inv*r2inv;
r8inv = r4inv*r4inv;
fwall = side * (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
+ 63.0*rad4*rad*pow(delta,4.0)
+ 21.0*rad2*rad*pow(delta,6.0))*r8inv -
new_coeff2*r2inv);
+ 63.0*rad4*rad*pow(delta,4.0)
+ 21.0*rad2*rad*pow(delta,6.0))*r8inv -
new_coeff2*r2inv);
f[i][dim] -= fwall;
r2 = rad - delta;
@ -131,9 +131,9 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
r4inv3 = r2inv3*r2inv3;
r6inv3 = r4inv3*r2inv3;
ewall[0] += coeff3[m]*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
+ (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3);
+ (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3);
// offset depends on particle size
@ -147,9 +147,9 @@ void FixWallColloid::wall_particle(int m, int which, double coord)
r4inv3 = r2inv3*r2inv3;
r6inv3 = r4inv3*r2inv3;
eoffset = coeff3[m]*((-3.5*diam+cutoff[m])*r4inv2*r2inv2*rinv2
+ (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3);
+ (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3);
ewall[0] -= eoffset;
ewall[m+1] += fwall;

2
src/COLLOID/fix_wall_colloid.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

212
src/COLLOID/pair_colloid.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -50,7 +50,7 @@ PairColloid::~PairColloid()
memory->destroy(a1);
memory->destroy(a2);
memory->destroy(diameter);
memory->destroy(cut);
memory->destroy(cut);
memory->destroy(offset);
memory->destroy(sigma3);
memory->destroy(sigma6);
@ -87,7 +87,7 @@ void PairColloid::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -103,7 +103,7 @@ void PairColloid::compute(int eflag, int vflag)
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@ -113,87 +113,87 @@ void PairColloid::compute(int eflag, int vflag)
if (rsq >= cutsq[itype][jtype]) continue;
switch (form[itype][jtype]) {
case SMALL_SMALL:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
if (eflag) evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
break;
case SMALL_SMALL:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
if (eflag) evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
break;
case SMALL_LARGE:
c2 = a2[itype][jtype];
K[1] = c2*c2;
K[2] = rsq;
K[0] = K[1] - rsq;
K[4] = rsq*rsq;
K[3] = K[1] - K[2];
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
fpair = 4.0/15.0*fR*factor_lj *
(2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6]-5.0) / K[0];
if (eflag)
evdwl = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
if (rsq <= K[1]) error->one(FLERR,"Overlapping small/large in pair colloid");
break;
c2 = a2[itype][jtype];
K[1] = c2*c2;
K[2] = rsq;
K[0] = K[1] - rsq;
K[4] = rsq*rsq;
K[3] = K[1] - K[2];
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
fpair = 4.0/15.0*fR*factor_lj *
(2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6]-5.0) / K[0];
if (eflag)
evdwl = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
if (rsq <= K[1]) error->one(FLERR,"Overlapping small/large in pair colloid");
break;
case LARGE_LARGE:
r = sqrt(rsq);
c1 = a1[itype][jtype];
c2 = a2[itype][jtype];
K[0] = c1*c2;
K[1] = c1+c2;
K[2] = c1-c2;
K[3] = K[1]+r;
K[4] = K[1]-r;
K[5] = K[2]+r;
K[6] = K[2]-r;
K[7] = 1.0/(K[3]*K[4]);
K[8] = 1.0/(K[5]*K[6]);
g[0] = pow(K[3],-7.0);
g[1] = pow(K[4],-7.0);
g[2] = pow(K[5],-7.0);
g[3] = pow(K[6],-7.0);
h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
fpair = factor_lj * (dUR+dUA)/r;
if (eflag)
evdwl += a12[itype][jtype]/6.0 *
(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
if (r <= K[1]) error->one(FLERR,"Overlapping large/large in pair colloid");
break;
r = sqrt(rsq);
c1 = a1[itype][jtype];
c2 = a2[itype][jtype];
K[0] = c1*c2;
K[1] = c1+c2;
K[2] = c1-c2;
K[3] = K[1]+r;
K[4] = K[1]-r;
K[5] = K[2]+r;
K[6] = K[2]-r;
K[7] = 1.0/(K[3]*K[4]);
K[8] = 1.0/(K[5]*K[6]);
g[0] = pow(K[3],-7.0);
g[1] = pow(K[4],-7.0);
g[2] = pow(K[5],-7.0);
g[3] = pow(K[6],-7.0);
h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
fpair = factor_lj * (dUR+dUA)/r;
if (eflag)
evdwl += a12[itype][jtype]/6.0 *
(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
if (r <= K[1]) error->one(FLERR,"Overlapping large/large in pair colloid");
break;
}
if (eflag) evdwl *= factor_lj;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
evdwl,0.0,fpair,delx,dely,delz);
}
}
@ -201,7 +201,7 @@ void PairColloid::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairColloid::allocate()
@ -235,7 +235,7 @@ void PairColloid::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairColloid::settings(int narg, char **arg)
@ -250,7 +250,7 @@ void PairColloid::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
@ -275,7 +275,7 @@ void PairColloid::coeff(int narg, char **arg)
double cut_one = cut_global;
if (narg == 7) cut_one = force->numeric(arg[6]);
if (d1_one < 0.0 || d2_one < 0.0)
if (d1_one < 0.0 || d2_one < 0.0)
error->all(FLERR,"Invalid d1 or d2 value for pair colloid coeff");
int count = 0;
@ -284,7 +284,7 @@ void PairColloid::coeff(int narg, char **arg)
a12[i][j] = a12_one;
sigma[i][j] = sigma_one;
if (i == j && d1_one != d2_one)
error->all(FLERR,"Invalid d1 or d2 value for pair colloid coeff");
error->all(FLERR,"Invalid d1 or d2 value for pair colloid coeff");
d1[i][j] = d1_one;
d2[i][j] = d2_one;
diameter[i][j] = 0.5*(d1_one+d2_one);
@ -349,7 +349,7 @@ double PairColloid::init_one(int i, int j)
offset[j][i] = offset[i][j] = 0.0;
if (offset_flag) {
double tmp;
offset[j][i] = offset[i][j] =
offset[j][i] = offset[i][j] =
single(0,0,i,j,cut[i][j]*cut[i][j],0.0,1.0,tmp);
}
@ -357,7 +357,7 @@ double PairColloid::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairColloid::write_restart(FILE *fp)
@ -369,11 +369,11 @@ void PairColloid::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a12[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&d1[i][j],sizeof(double),1,fp);
fwrite(&d2[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&a12[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&d1[i][j],sizeof(double),1,fp);
fwrite(&d2[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@ -394,18 +394,18 @@ void PairColloid::read_restart(FILE *fp)
if (comm->me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (comm->me == 0) {
fread(&a12[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&d1[i][j],sizeof(double),1,fp);
fread(&d2[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d2[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (comm->me == 0) {
fread(&a12[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&d1[i][j],sizeof(double),1,fp);
fread(&d2[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d2[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -441,8 +441,8 @@ void PairColloid::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
double factor_coul, double factor_lj,
double &fforce)
{
double K[9],h[4],g[4];
double r,r2inv,r6inv,forcelj,c1,c2,phi,fR,dUR,dUA;
@ -467,11 +467,11 @@ double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
fforce = 4.0/15.0*fR*factor_lj *
(2.0*(K[1]+K[2])*(K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
fforce = 4.0/15.0*fR*factor_lj *
(2.0*(K[1]+K[2])*(K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6] - 5.0)/K[0];
phi = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
phi = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
break;
@ -500,14 +500,14 @@ double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
phi = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = phi/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
fforce = factor_lj*(dUR+dUA)/r;
phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
offset[itype][jtype];
break;
}

2
src/COLLOID/pair_colloid.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

60
src/COLLOID/pair_yukawa_colloid.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -58,7 +58,7 @@ void PairYukawaColloid::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -82,32 +82,32 @@ void PairYukawaColloid::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
radj = radius[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(radi+radj)));
forceyukawa = a[itype][jtype] * screening;
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(radi+radj)));
forceyukawa = a[itype][jtype] * screening;
fpair = factor*forceyukawa * rinv;
fpair = factor*forceyukawa * rinv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
evdwl *= factor;
}
if (eflag) {
evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
evdwl *= factor;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
@ -123,7 +123,7 @@ void PairYukawaColloid::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair yukawa/colloid requires atom style sphere");
neighbor->request(this);
// require that atom radii are identical within each type
@ -131,7 +131,7 @@ void PairYukawaColloid::init_style()
for (int i = 1; i <= atom->ntypes; i++)
if (!atom->radius_consistency(i,rad[i]))
error->all(FLERR,"Pair yukawa/colloid requires atoms with same type "
"have same radius");
"have same radius");
}
/* ----------------------------------------------------------------------
@ -159,12 +159,12 @@ double PairYukawaColloid::init_one(int i, int j)
/* ---------------------------------------------------------------------- */
double PairYukawaColloid::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi;
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
@ -172,6 +172,6 @@ double PairYukawaColloid::single(int i, int j, int itype, int jtype,
forceyukawa = a[itype][jtype] * screening;
fforce = factor_lj*forceyukawa * rinv;
phi = a[itype][jtype]/kappa * screening - offset[itype][jtype];
phi = a[itype][jtype]/kappa * screening - offset[itype][jtype];
return factor_lj*phi;
}

2
src/COLLOID/pair_yukawa_colloid.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

168
src/DIPOLE/atom_vec_dipole.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -50,7 +50,7 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecDipole::grow(int n)
@ -73,7 +73,7 @@ void AtomVecDipole::grow(int n)
mu = memory->grow(atom->mu,nmax,4,"atom:mu");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
@ -113,14 +113,14 @@ void AtomVecDipole::copy(int i, int j, int delflag)
mu[j][3] = mu[i][3];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@ -162,7 +162,7 @@ int AtomVecDipole::pack_comm(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_comm_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -193,38 +193,38 @@ int AtomVecDipole::pack_comm_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
}
}
@ -336,7 +336,7 @@ void AtomVecDipole::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz;
@ -388,7 +388,7 @@ int AtomVecDipole::pack_border(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
int AtomVecDipole::pack_border_vel(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
double dx,dy,dz,dvx,dvy,dvz;
@ -424,48 +424,48 @@ int AtomVecDipole::pack_border_vel(int n, int *list, double *buf,
}
if (!deform_vremap) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = mu[j][3];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = mu[j][3];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
dvz = pbc[2]*h_rate[2];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = mu[j][3];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
j = list[i];
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = mu[j][3];
if (mask[i] & deform_groupbit) {
buf[m++] = v[j][0] + dvx;
buf[m++] = v[j][1] + dvy;
buf[m++] = v[j][2] + dvz;
} else {
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
}
}
@ -585,7 +585,7 @@ int AtomVecDipole::pack_exchange(int i, double *buf)
buf[m++] = mu[i][3];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
@ -618,9 +618,9 @@ int AtomVecDipole::unpack_exchange(double *buf)
mu[nlocal][3] = buf[m++];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
m += modify->fix[atom->extra_grow[iextra]]->
unpack_exchange(nlocal,&buf[m]);
unpack_exchange(nlocal,&buf[m]);
atom->nlocal++;
return m;
@ -639,9 +639,9 @@ int AtomVecDipole::size_restart()
int n = 16 * nlocal;
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (i = 0; i < nlocal; i++)
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
return n;
}
@ -649,7 +649,7 @@ int AtomVecDipole::size_restart()
/* ----------------------------------------------------------------------
pack atom I's data for restart file including extra quantities
xyz must be 1st 3 values, so that read_restart can test on them
molecular types may be negative, but write as positive
molecular types may be negative, but write as positive
------------------------------------------------------------------------- */
int AtomVecDipole::pack_restart(int i, double *buf)
@ -673,7 +673,7 @@ int AtomVecDipole::pack_restart(int i, double *buf)
buf[m++] = mu[i][3];
if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
buf[0] = m;
@ -778,9 +778,9 @@ void AtomVecDipole::data_atom(double *coord, int imagetmp, char **values)
mu[nlocal][0] = atof(values[6]);
mu[nlocal][1] = atof(values[7]);
mu[nlocal][2] = atof(values[8]);
mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
mu[nlocal][1]*mu[nlocal][1] +
mu[nlocal][2]*mu[nlocal][2]);
mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
mu[nlocal][1]*mu[nlocal][1] +
mu[nlocal][2]*mu[nlocal][2]);
image[nlocal] = imagetmp;
@ -803,14 +803,14 @@ int AtomVecDipole::data_atom_hybrid(int nlocal, char **values)
mu[nlocal][0] = atof(values[1]);
mu[nlocal][1] = atof(values[2]);
mu[nlocal][2] = atof(values[3]);
mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
mu[nlocal][1]*mu[nlocal][1] +
mu[nlocal][2]*mu[nlocal][2]);
mu[nlocal][3] = sqrt(mu[nlocal][0]*mu[nlocal][0] +
mu[nlocal][1]*mu[nlocal][1] +
mu[nlocal][2]*mu[nlocal][2]);
return 4;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
return # of bytes of allocated memory
------------------------------------------------------------------------- */
bigint AtomVecDipole::memory_usage()

2
src/DIPOLE/atom_vec_dipole.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

250
src/DIPOLE/pair_dipole_cut.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -86,7 +86,7 @@ void PairDipoleCut::compute(int eflag, int vflag)
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
@ -112,142 +112,142 @@ void PairDipoleCut::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
// atom can have both a charge and dipole
// i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
// atom can have both a charge and dipole
// i,j = charge-charge, dipole-dipole, dipole-charge, or charge-dipole
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
if (rsq < cut_coulsq[itype][jtype]) {
forcecoulx = forcecouly = forcecoulz = 0.0;
tixcoul = tiycoul = tizcoul = 0.0;
tjxcoul = tjycoul = tjzcoul = 0.0;
if (qtmp != 0.0 && q[j] != 0.0) {
if (rsq < cut_coulsq[itype][jtype]) {
if (qtmp != 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
pre1 = qtmp*q[j]*r3inv;
pre1 = qtmp*q[j]*r3inv;
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
forcecoulz += pre1*delz;
}
forcecoulx += pre1*delx;
forcecouly += pre1*dely;
forcecoulz += pre1*delz;
}
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
if (mu[i][3] > 0.0 && mu[j][3] > 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
r7inv = r5inv*r2inv;
r7inv = r5inv*r2inv;
pdotp = mu[i][0]*mu[j][0] + mu[i][1]*mu[j][1] + mu[i][2]*mu[j][2];
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
pre2 = 3.0*r5inv*pjdotr;
pre3 = 3.0*r5inv*pidotr;
pre4 = -1.0*r3inv;
pre1 = 3.0*r5inv*pdotp - 15.0*r7inv*pidotr*pjdotr;
pre2 = 3.0*r5inv*pjdotr;
pre3 = 3.0*r5inv*pidotr;
pre4 = -1.0*r3inv;
forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
forcecoulx += pre1*delx + pre2*mu[i][0] + pre3*mu[j][0];
forcecouly += pre1*dely + pre2*mu[i][1] + pre3*mu[j][1];
forcecoulz += pre1*delz + pre2*mu[i][2] + pre3*mu[j][2];
tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
}
crossx = pre4 * (mu[i][1]*mu[j][2] - mu[i][2]*mu[j][1]);
crossy = pre4 * (mu[i][2]*mu[j][0] - mu[i][0]*mu[j][2]);
crossz = pre4 * (mu[i][0]*mu[j][1] - mu[i][1]*mu[j][0]);
if (mu[i][3] > 0.0 && q[j] != 0.0) {
tixcoul += crossx + pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += crossy + pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += crossz + pre2 * (mu[i][0]*dely - mu[i][1]*delx);
tjxcoul += -crossx + pre3 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -crossy + pre3 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -crossz + pre3 * (mu[j][0]*dely - mu[j][1]*delx);
}
if (mu[i][3] > 0.0 && q[j] != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pidotr = mu[i][0]*delx + mu[i][1]*dely + mu[i][2]*delz;
pre1 = 3.0*q[j]*r5inv * pidotr;
pre2 = q[j]*r3inv;
pre1 = 3.0*q[j]*r5inv * pidotr;
pre2 = q[j]*r3inv;
forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecoulx += pre2*mu[i][0] - pre1*delx;
forcecouly += pre2*mu[i][1] - pre1*dely;
forcecoulz += pre2*mu[i][2] - pre1*delz;
tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
}
tixcoul += pre2 * (mu[i][1]*delz - mu[i][2]*dely);
tiycoul += pre2 * (mu[i][2]*delx - mu[i][0]*delz);
tizcoul += pre2 * (mu[i][0]*dely - mu[i][1]*delx);
}
if (mu[j][3] > 0.0 && qtmp != 0.0) {
if (mu[j][3] > 0.0 && qtmp != 0.0) {
r3inv = r2inv*rinv;
r5inv = r3inv*r2inv;
pjdotr = mu[j][0]*delx + mu[j][1]*dely + mu[j][2]*delz;
pre1 = 3.0*qtmp*r5inv * pjdotr;
pre2 = qtmp*r3inv;
pre1 = 3.0*qtmp*r5inv * pjdotr;
pre2 = qtmp*r3inv;
forcecoulx += pre1*delx - pre2*mu[j][0];
forcecoulx += pre1*delx - pre2*mu[j][0];
forcecouly += pre1*dely - pre2*mu[j][1];
forcecoulz += pre1*delz - pre2*mu[j][2];
tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
}
}
tjxcoul += -pre2 * (mu[j][1]*delz - mu[j][2]*dely);
tjycoul += -pre2 * (mu[j][2]*delx - mu[j][0]*delz);
tjzcoul += -pre2 * (mu[j][0]*dely - mu[j][1]*delx);
}
}
// LJ interaction
// LJ interaction
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= factor_lj * r2inv;
} else forcelj = 0.0;
// total force
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= factor_lj * r2inv;
} else forcelj = 0.0;
fq = factor_coul*qqrd2e;
fx = fq*forcecoulx + delx*forcelj;
fy = fq*forcecouly + dely*forcelj;
fz = fq*forcecoulz + delz*forcelj;
// force & torque accumulation
// total force
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
torque[i][0] += fq*tixcoul;
torque[i][1] += fq*tiycoul;
torque[i][2] += fq*tizcoul;
fq = factor_coul*qqrd2e;
fx = fq*forcecoulx + delx*forcelj;
fy = fq*forcecouly + dely*forcelj;
fz = fq*forcecoulz + delz*forcelj;
if (newton_pair || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
torque[j][0] += fq*tjxcoul;
torque[j][1] += fq*tjycoul;
torque[j][2] += fq*tjzcoul;
}
// force & torque accumulation
if (eflag) {
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = qtmp*q[j]*rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j]*r3inv*pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp*r3inv*pjdotr;
ecoul *= factor_coul*qqrd2e;
} else ecoul = 0.0;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
torque[i][0] += fq*tixcoul;
torque[i][1] += fq*tiycoul;
torque[i][2] += fq*tizcoul;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (newton_pair || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
torque[j][0] += fq*tjxcoul;
torque[j][1] += fq*tjycoul;
torque[j][2] += fq*tjzcoul;
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,ecoul,fx,fy,fz,delx,dely,delz);
if (eflag) {
if (rsq < cut_coulsq[itype][jtype]) {
ecoul = qtmp*q[j]*rinv;
if (mu[i][3] > 0.0 && mu[j][3] > 0.0)
ecoul += r3inv*pdotp - 3.0*r5inv*pidotr*pjdotr;
if (mu[i][3] > 0.0 && q[j] != 0.0)
ecoul += -q[j]*r3inv*pidotr;
if (mu[j][3] > 0.0 && qtmp != 0.0)
ecoul += qtmp*r3inv*pjdotr;
ecoul *= factor_coul*qqrd2e;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
evdwl,ecoul,fx,fy,fz,delx,dely,delz);
}
}
}
@ -256,7 +256,7 @@ void PairDipoleCut::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairDipoleCut::allocate()
@ -285,7 +285,7 @@ void PairDipoleCut::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairDipoleCut::settings(int narg, char **arg)
@ -303,10 +303,10 @@ void PairDipoleCut::settings(int narg, char **arg)
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
if (setflag[i][j]) {
cut_lj[i][j] = cut_lj_global;
cut_coul[i][j] = cut_coul_global;
}
}
}
@ -316,7 +316,7 @@ void PairDipoleCut::settings(int narg, char **arg)
void PairDipoleCut::coeff(int narg, char **arg)
{
if (narg < 4 || narg > 6)
if (narg < 4 || narg > 6)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
@ -367,7 +367,7 @@ double PairDipoleCut::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
@ -381,12 +381,12 @@ double PairDipoleCut::init_one(int i, int j)
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
cut_coulsq[j][i] = cut_coulsq[i][j];
lj1[j][i] = lj1[i][j];
@ -411,10 +411,10 @@ void PairDipoleCut::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
}
}
}
@ -436,16 +436,16 @@ void PairDipoleCut::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&cut_lj[i][j],sizeof(double),1,fp);
fread(&cut_coul[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
}
}
}

2
src/DIPOLE/pair_dipole_cut.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

272
src/FLD/pair_brownian.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -104,37 +104,37 @@ void PairBrownian::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
@ -156,8 +156,8 @@ void PairBrownian::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
jnum = numneigh[i];
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
@ -165,12 +165,12 @@ void PairBrownian::compute(int eflag, int vflag)
f[i][1] += prethermostat*sqrt(R0)*(random->uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0)*(random->uniform()-0.5);
if (flaglog) {
torque[i][0] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][0] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
}
}
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@ -184,25 +184,25 @@ void PairBrownian::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
r = sqrt(rsq);
// scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
// check for overlaps
if (h_sep < 0.0) overlaps++;
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - 2.0*radi;
h_sep = cut_inner[itype][jtype] - 2.0*radi;
// scale h_sep by radi
h_sep = h_sep/radi;
// scalar resistances
if (flaglog) {
@ -211,70 +211,70 @@ void PairBrownian::compute(int eflag, int vflag)
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
// generate a random number
randr = random->uniform()-0.5;
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
// add terms due to a_sh
if (flaglog) {
// generate two orthogonal vectors to the line of centers
p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
// magnitude
Fbmag = prethermostat*sqrt(a_sh);
Fbmag = prethermostat*sqrt(a_sh);
// force in each of the two directions
randr = random->uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
randr = random->uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
fz += Fbmag*randr*p3[2];
}
fz += Fbmag*randr*p3[2];
}
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// sum to total force
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
f[i][2] -= fz;
if (newton_pair || j < nlocal) {
//randr = random->uniform()-0.5;
//fx = Fbmag*randr*delx/r;
//fy = Fbmag*randr*dely/r;
//fz = Fbmag*randr*delz/r;
if (newton_pair || j < nlocal) {
//randr = random->uniform()-0.5;
//fx = Fbmag*randr*delx/r;
//fy = Fbmag*randr*dely/r;
//fz = Fbmag*randr*delz/r;
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
}
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
}
// torque due to the Brownian Force
if (flaglog) {
@ -284,56 +284,56 @@ void PairBrownian::compute(int eflag, int vflag)
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
tz = xl[0]*fy - xl[1]*fx;
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
torque[i][2] -= tz;
if (newton_pair || j < nlocal) {
torque[j][0] -= tx;
torque[j][1] -= ty;
torque[j][2] -= tz;
}
torque[i][2] -= tz;
if (newton_pair || j < nlocal) {
torque[j][0] -= tx;
torque[j][1] -= ty;
torque[j][2] -= tz;
}
// torque due to a_pu
Fbmag = prethermostat*sqrt(a_pu);
Fbmag = prethermostat*sqrt(a_pu);
// force in each direction
randr = random->uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
randr = random->uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
tz += Fbmag*randr*p3[2];
tz += Fbmag*randr*p3[2];
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
torque[i][2] -= tz;
if (newton_pair || j < nlocal) {
torque[j][0] += tx;
torque[j][1] += ty;
torque[j][2] += tz;
}
torque[i][2] -= tz;
if (newton_pair || j < nlocal) {
torque[j][0] += tx;
torque[j][1] += ty;
torque[j][2] += tz;
}
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
@ -346,7 +346,7 @@ void PairBrownian::compute(int eflag, int vflag)
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairBrownian::allocate()
@ -366,7 +366,7 @@ void PairBrownian::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairBrownian::settings(int narg, char **arg)
@ -374,12 +374,12 @@ void PairBrownian::settings(int narg, char **arg)
if (narg != 7 && narg != 9) error->all(FLERR,"Illegal pair_style command");
mu = atof(arg[0]);
flaglog = atoi(arg[1]);
flagfld = atoi(arg[2]);
cut_inner_global = atof(arg[3]);
cut_global = atof(arg[4]);
t_target = atof(arg[5]);
seed = atoi(arg[6]);
flaglog = atoi(arg[1]);
flagfld = atoi(arg[2]);
cut_inner_global = atof(arg[3]);
cut_global = atof(arg[4]);
t_target = atof(arg[5]);
seed = atoi(arg[6]);
flagHI = flagVF = 1;
if (narg == 9) {
@ -389,9 +389,9 @@ void PairBrownian::settings(int narg, char **arg)
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
"setting flagHI to 1");
"setting flagHI to 1");
flagHI = 1;
}
}
// initialize Marsaglia RNG with processor-unique seed
@ -427,7 +427,7 @@ void PairBrownian::coeff(int narg, char **arg)
double cut_inner_one = cut_inner_global;
double cut_one = cut_global;
if (narg == 4) {
cut_inner_one = atof(arg[2]);
cut_one = atof(arg[3]);
@ -459,8 +459,8 @@ void PairBrownian::init_style()
if (force->newton_pair == 0 && comm->me == 0)
error->warning(FLERR,
"Pair brownian needs newton pair on for "
"momentum conservation");
"Pair brownian needs newton pair on for "
"momentum conservation");
int irequest = neighbor->request(this);
@ -472,7 +472,7 @@ void PairBrownian::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (radius[i] == 0.0)
if (radius[i] == 0.0)
error->one(FLERR,"Pair brownian requires extended particles");
// require monodisperse system with same radii for all types
@ -485,7 +485,7 @@ void PairBrownian::init_style()
error->all(FLERR,"Pair brownian requires monodisperse particles");
rad = radtype;
}
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
// check for fix deform, if exists it must use "remap v"
@ -499,52 +499,52 @@ void PairBrownian::init_style()
flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0)
if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
}
}
// set the isotropic constants depending on the volume fraction
// vol_T = total volumeshearing = flagdeform = flagwall = 0;
// vol_T = total volumeshearing = flagdeform = flagwall = 0;
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
else {
else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
// vol_P = volume of particles, assuming mono-dispersity
// vol_f = volume fraction
vol_P = atom->natoms*(4.0/3.0)*MY_PI*pow(rad,3.0);
double vol_f = vol_P/vol_T;
// set isotropic constants
if (!flagVF) vol_f = 0;
@ -553,7 +553,7 @@ void PairBrownian::init_style()
RT0 = 8*MY_PI*mu*pow(rad,3.0); // not actually needed
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
}
}
@ -574,7 +574,7 @@ double PairBrownian::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBrownian::write_restart(FILE *fp)
@ -586,8 +586,8 @@ void PairBrownian::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@ -608,12 +608,12 @@ void PairBrownian::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -678,11 +678,11 @@ void PairBrownian::read_restart_settings(FILE *fp)
/* ----------------------------------------------------------------------*/
void PairBrownian::set_3_orthogonal_vectors(double p1[3],
double p2[3], double p3[3])
double p2[3], double p3[3])
{
double norm;
int ix,iy,iz;
// find the index of maximum magnitude and store it in iz
if (fabs(p1[0]) > fabs(p1[1])) {
@ -694,7 +694,7 @@ void PairBrownian::set_3_orthogonal_vectors(double p1[3],
ix=2;
iy=0;
}
if (iz==0) {
if (fabs(p1[0]) < fabs(p1[2])) {
iz = 2;
@ -708,24 +708,24 @@ void PairBrownian::set_3_orthogonal_vectors(double p1[3],
iy = 1;
}
}
// set p2 arbitrarily such that it's orthogonal to p1
p2[ix]=1.0;
p2[iy]=1.0;
p2[iy]=1.0;
p2[iz] = -(p1[ix]*p2[ix] + p1[iy]*p2[iy])/p1[iz];
// normalize p2
norm = sqrt(p2[0]*p2[0] + p2[1]*p2[1] + p2[2]*p2[2]);
p2[0] = p2[0]/norm;
p2[1] = p2[1]/norm;
p2[2] = p2[2]/norm;
// Set p3 by taking the cross product p3=p2xp1
p3[0] = p1[1]*p2[2] - p1[2]*p2[1];
p3[1] = p1[2]*p2[0] - p1[0]*p2[2];
p3[2] = p1[0]*p2[1] - p1[1]*p2[0];
p3[2] = p1[0]*p2[1] - p1[1]*p2[0];
}

6
src/FLD/pair_brownian.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -28,7 +28,7 @@ class PairBrownian : public Pair {
public:
PairBrownian(class LAMMPS *);
virtual ~PairBrownian();
virtual void compute(int, int);
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
virtual double init_one(int, int);
@ -36,7 +36,7 @@ class PairBrownian : public Pair {
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void read_restart_settings(FILE *);
protected:
double cut_inner_global,cut_global;

194
src/FLD/pair_brownian_poly.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -81,7 +81,7 @@ void PairBrownianPoly::compute(int eflag, int vflag)
double prethermostat;
double xl[3],a_sq,a_sh,a_pu,Fbmag;
double p1[3],p2[3],p3[3];
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@ -90,37 +90,37 @@ void PairBrownianPoly::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
double wallhi[3], walllo[3];
for (j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
double wallhi[3], walllo[3];
for (j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// scale factor for Brownian moments
@ -142,8 +142,8 @@ void PairBrownianPoly::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
jnum = numneigh[i];
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
@ -151,16 +151,16 @@ void PairBrownianPoly::compute(int eflag, int vflag)
f[i][1] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
if (flaglog) {
const double radi3 = radi*radi*radi;
torque[i][0] += prethermostat*sqrt(RT0*radi3) *
(random->uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0*radi3) *
(random->uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0*radi3) *
(random->uniform()-0.5);
const double radi3 = radi*radi*radi;
torque[i][0] += prethermostat*sqrt(RT0*radi3) *
(random->uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0*radi3) *
(random->uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0*radi3) *
(random->uniform()-0.5);
}
}
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
@ -175,99 +175,99 @@ void PairBrownianPoly::compute(int eflag, int vflag)
radj = radius[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
r = sqrt(rsq);
// scalar resistances a_sq and a_sh
h_sep = r - radi-radj;
// check for overlaps
if (h_sep < 0.0) overlaps++;
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - radi-radj;
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
// scalar resistances
if (flaglog) {
a_sq = beta0*beta0/beta1/beta1/h_sep +
(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
pow(beta0,4.0))/21.0/pow(beta1,4.0)*h_sep*log(1.0/h_sep);
a_sq = beta0*beta0/beta1/beta1/h_sep +
(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
pow(beta0,4.0))/21.0/pow(beta1,4.0)*h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
h_sep*log(1.0/h_sep);
a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
// generate a random number
randr = random->uniform()-0.5;
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
// add terms due to a_sh
if (flaglog) {
// generate two orthogonal vectors to the line of centers
p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
// magnitude
Fbmag = prethermostat*sqrt(a_sh);
Fbmag = prethermostat*sqrt(a_sh);
// force in each of the two directions
randr = random->uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
randr = random->uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
fz += Fbmag*randr*p3[2];
}
fz += Fbmag*randr*p3[2];
}
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// sum to total Force
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
f[i][2] -= fz;
// torque due to the Brownian Force
@ -278,47 +278,47 @@ void PairBrownianPoly::compute(int eflag, int vflag)
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
tz = xl[0]*fy - xl[1]*fx;
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
torque[i][2] -= tz;
torque[i][2] -= tz;
// torque due to a_pu
Fbmag = prethermostat*sqrt(a_pu);
Fbmag = prethermostat*sqrt(a_pu);
// force in each direction
randr = random->uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
randr = random->uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
tz += Fbmag*randr*p3[2];
tz += Fbmag*randr*p3[2];
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
torque[i][2] -= tz;
torque[i][2] -= tz;
}
// set j = nlocal so that only I gets tallied
// set j = nlocal so that only I gets tallied
if (evflag) ev_tally_xyz(i,nlocal,nlocal,0,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
@ -343,61 +343,61 @@ void PairBrownianPoly::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (radius[i] == 0.0)
if (radius[i] == 0.0)
error->one(FLERR,"Pair brownian/poly requires extended particles");
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
else {
else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
// vol_P = volume of particles, assuming mono-dispersity
// vol_f = volume fraction
double volP = 0.0;
for (int i = 0; i < nlocal; i++)
volP += (4.0/3.0)*MY_PI*pow(atom->radius[i],3.0);
volP += (4.0/3.0)*MY_PI*pow(atom->radius[i],3.0);
MPI_Allreduce(&volP,&vol_P,1,MPI_DOUBLE,MPI_SUM,world);
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
// set isotropic constants
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
} else {
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
}
}
@ -412,6 +412,6 @@ double PairBrownianPoly::init_one(int i, int j)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
cut_inner[j][i] = cut_inner[i][j];
cut_inner[j][i] = cut_inner[i][j];
return cut[i][j];
}

4
src/FLD/pair_brownian_poly.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -28,7 +28,7 @@ class PairBrownianPoly : public PairBrownian {
public:
PairBrownianPoly(class LAMMPS *);
~PairBrownianPoly() {}
void compute(int, int);
void compute(int, int);
double init_one(int, int);
void init_style();
};

248
src/FLD/pair_lubricate.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -84,7 +84,7 @@ void PairLubricate::compute(int eflag, int vflag)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double inertia,inv_inertia,vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3];
double a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
@ -110,7 +110,7 @@ void PairLubricate::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
int overlaps = 0;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@ -134,10 +134,10 @@ void PairLubricate::compute(int eflag, int vflag)
i = ilist[ii];
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
@ -153,7 +153,7 @@ void PairLubricate::compute(int eflag, int vflag)
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
Ef[2][2] = h_rate[2]/domain->zprd;
Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
@ -163,7 +163,7 @@ void PairLubricate::compute(int eflag, int vflag)
comm->forward_comm_pair(this);
}
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@ -171,45 +171,45 @@ void PairLubricate::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// end of R0 adjustment code
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@ -219,30 +219,30 @@ void PairLubricate::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
jnum = numneigh[i];
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
wi[2] = omega[i][2];
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
if (flagfld) {
f[i][0] -= vxmu2f*R0*v[i][0];
f[i][1] -= vxmu2f*R0*v[i][1];
f[i][2] -= vxmu2f*R0*v[i][2];
f[i][2] -= vxmu2f*R0*v[i][2];
torque[i][0] -= vxmu2f*RT0*wi[0];
torque[i][1] -= vxmu2f*RT0*wi[1];
torque[i][2] -= vxmu2f*RT0*wi[2];
torque[i][2] -= vxmu2f*RT0*wi[2];
if (shearing && vflag_either) {
vRS0 = -vxmu2f * RS0;
v_tally_tensor(i,i,nlocal,newton_pair,
vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
vRS0 = -vxmu2f * RS0;
v_tally_tensor(i,i,nlocal,newton_pair,
vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
}
}
@ -259,20 +259,20 @@ void PairLubricate::compute(int eflag, int vflag)
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
r = sqrt(rsq);
// angular momentum = I*omega = 2/5 * M*R^2 * omega
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
// xl = point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl - Ef.xl
@ -280,41 +280,41 @@ void PairLubricate::compute(int eflag, int vflag)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1])
+ (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2])
+ (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0])
+ (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// scalar resistances XA and YA
h_sep = r - 2.0*radi;
// check for overlaps
if (h_sep < 0.0) overlaps++;
// if less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - 2.0*radi;
h_sep = cut_inner[itype][jtype] - 2.0*radi;
// scale h_sep by radi
h_sep = h_sep/radi;
// scalar resistances
if (flaglog) {
@ -323,14 +323,14 @@ void PairLubricate::compute(int eflag, int vflag)
a_pu = 8.0*MY_PI*mu*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
// relative velocity at the point of closest approach
// includes fluid velocity
// includes fluid velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
// normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@ -355,7 +355,7 @@ void PairLubricate::compute(int eflag, int vflag)
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
fz = fz + a_sh*vt3;
}
// scale forces for appropriate units
@ -363,65 +363,65 @@ void PairLubricate::compute(int eflag, int vflag)
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
// add to total force
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
f[i][2] -= fz;
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
f[j][2] += fz;
}
// torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
tz = xl[0]*fy - xl[1]*fx;
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
torque[i][2] -= vxmu2f*tz;
if (newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
// torque due to a_pu
wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
(wi[2]-wj[2])*delz)/r;
wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
(wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
torque[i][2] -= vxmu2f*tz;
if (newton_pair || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
}
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
// restore streaming component of velocity, omega, angmom
if (shearing) {
@ -432,10 +432,10 @@ void PairLubricate::compute(int eflag, int vflag)
i = ilist[ii];
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
@ -457,12 +457,12 @@ void PairLubricate::compute(int eflag, int vflag)
if (overlaps_all && comm->me == 0)
printf("Number of overlaps = %d\n",overlaps);
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
allocate all arrays
------------------------------------------------------------------------- */
void PairLubricate::allocate()
@ -482,7 +482,7 @@ void PairLubricate::allocate()
}
/* ----------------------------------------------------------------------
global settings
global settings
------------------------------------------------------------------------- */
void PairLubricate::settings(int narg, char **arg)
@ -503,9 +503,9 @@ void PairLubricate::settings(int narg, char **arg)
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
"setting flagHI to 1");
"setting flagHI to 1");
flagHI = 1;
}
}
// reset cutoffs that have been explicitly set
@ -587,51 +587,51 @@ void PairLubricate::init_style()
// due to walls, set volume appropriately; if walls will
// move, set appropriate flag so that volume and v.f. corrections
// are re-calculated at every step.
shearing = flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = flagdeform = 1;
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using pair lubricate with inconsistent "
"fix deform remap option");
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using pair lubricate with inconsistent "
"fix deform remap option");
}
if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
}
}
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
double vol_T;
double wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
else {
else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
@ -642,16 +642,16 @@ void PairLubricate::init_style()
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
// set isotropic constants for FLD
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
@ -680,7 +680,7 @@ double PairLubricate::init_one(int i, int j)
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLubricate::write_restart(FILE *fp)
@ -692,8 +692,8 @@ void PairLubricate::write_restart(FILE *fp)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
@ -714,12 +714,12 @@ void PairLubricate::read_restart(FILE *fp)
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
@ -757,7 +757,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&flagHI,sizeof(int),1,fp);
fread(&flagVF,sizeof(int),1,fp);
fread(&flagVF,sizeof(int),1,fp);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flaglog,1,MPI_INT,0,world);
@ -773,7 +773,7 @@ void PairLubricate::read_restart_settings(FILE *fp)
/* ---------------------------------------------------------------------- */
int PairLubricate::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
int pbc_flag, int *pbc)
{
int i,j,m;
@ -834,7 +834,7 @@ int PairLubricate::pre_adapt(char *name, int ilo, int ihi, int jlo, int jhi)
------------------------------------------------------------------------- */
void PairLubricate::adapt(int which, int ilo, int ihi, int jlo, int jhi,
double value)
double value)
{
mu = value;
}

2
src/FLD/pair_lubricate.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

1088
src/FLD/pair_lubricateU.cpp
View File

File diff suppressed because it is too large Load Diff

2
src/FLD/pair_lubricateU.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

790
src/FLD/pair_lubricateU_poly.cpp
View File

File diff suppressed because it is too large Load Diff

2
src/FLD/pair_lubricateU_poly.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

234
src/FLD/pair_lubricate_poly.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -69,7 +69,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,h_sepj,beta0,beta1,betaj,betaj1,radi,radj,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double vt1,vt2,vt3,wt1,wt2,wt3,wdotn;
double inertia,inv_inertia,vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3],jl[3];
double a_sq,a_sh,a_pu,Fbmag,del,delmin,eta;
@ -95,7 +95,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
int overlaps = 0;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
@ -120,8 +120,8 @@ void PairLubricatePoly::compute(int eflag, int vflag)
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
@ -137,7 +137,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
Ef[2][2] = h_rate[2]/domain->zprd;
Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
@ -147,7 +147,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
comm->forward_comm_pair(this);
}
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
@ -155,43 +155,43 @@ void PairLubricatePoly::compute(int eflag, int vflag)
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// end of R0 adjustment code
// end of R0 adjustment code
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
@ -199,15 +199,15 @@ void PairLubricatePoly::compute(int eflag, int vflag)
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
jnum = numneigh[i];
radi = radius[i];
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
wi[2] = omega[i][2];
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
@ -215,21 +215,21 @@ void PairLubricatePoly::compute(int eflag, int vflag)
f[i][0] -= vxmu2f*R0*radi*v[i][0];
f[i][1] -= vxmu2f*R0*radi*v[i][1];
f[i][2] -= vxmu2f*R0*radi*v[i][2];
const double radi3 = radi*radi*radi;
const double radi3 = radi*radi*radi;
torque[i][0] -= vxmu2f*RT0*radi3*wi[0];
torque[i][1] -= vxmu2f*RT0*radi3*wi[1];
torque[i][2] -= vxmu2f*RT0*radi3*wi[2];
torque[i][2] -= vxmu2f*RT0*radi3*wi[2];
if (shearing && vflag_either) {
vRS0 = -vxmu2f * RS0*radi3;
v_tally_tensor(i,i,nlocal,newton_pair,
vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
vRS0 = -vxmu2f * RS0*radi3;
v_tally_tensor(i,i,nlocal,newton_pair,
vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][2]);
}
}
if (!flagHI) continue;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
delx = xtmp - x[j][0];
@ -240,13 +240,13 @@ void PairLubricatePoly::compute(int eflag, int vflag)
radj = atom->radius[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
r = sqrt(rsq);
// angular momentum = I*omega = 2/5 * M*R^2 * omega
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
// xl = point of closest approach on particle i from its center
@ -256,7 +256,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
jl[0] = -delx/r*radj;
jl[1] = -dely/r*radj;
jl[2] = -delz/r*radj;
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl - Ef.xl
@ -264,71 +264,71 @@ void PairLubricatePoly::compute(int eflag, int vflag)
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// particle j
vj[0] = v[j][0] - (wj[1]*jl[2] - wj[2]*jl[1])
+ (Ef[0][0]*jl[0] + Ef[0][1]*jl[1] + Ef[0][2]*jl[2]);
vj[1] = v[j][1] - (wj[2]*jl[0] - wj[0]*jl[2])
+ (Ef[1][0]*jl[0] + Ef[1][1]*jl[1] + Ef[1][2]*jl[2]);
vj[2] = v[j][2] - (wj[0]*jl[1] - wj[1]*jl[0])
+ (Ef[2][0]*jl[0] + Ef[2][1]*jl[1] + Ef[2][2]*jl[2]);
// scalar resistances XA and YA
h_sep = r - radi-radj;
// check for overlaps
if (h_sep < 0.0) overlaps++;
// if less than the minimum gap use the minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - radi-radj;
h_sep = cut_inner[itype][jtype] - radi-radj;
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
// scalar resistances
if (flaglog) {
a_sq = beta0*beta0/beta1/beta1/h_sep +
(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0 *
pow(beta0,3.0)+pow(beta0,4.0))/21.0/pow(beta1,4.0) *
h_sep*log(1.0/h_sep);
a_sq = beta0*beta0/beta1/beta1/h_sep +
(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3.0)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0 *
pow(beta0,3.0)+pow(beta0,4.0))/21.0/pow(beta1,4.0) *
h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
h_sep*log(1.0/h_sep);
a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3.0) *
log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
pow(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
// relative velocity at the point of closest approach
// includes fluid velocity
// includes fluid velocity
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
// normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
@ -353,7 +353,7 @@ void PairLubricatePoly::compute(int eflag, int vflag)
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
fz = fz + a_sh*vt3;
}
// scale forces for appropriate units
@ -361,50 +361,50 @@ void PairLubricatePoly::compute(int eflag, int vflag)
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
// add to total force
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
f[i][2] -= fz;
// torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
tz = xl[0]*fy - xl[1]*fx;
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
torque[i][2] -= vxmu2f*tz;
// torque due to a_pu
wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
(wi[2]-wj[2])*delz)/r;
wdotn = ((wi[0]-wj[0])*delx + (wi[1]-wj[1])*dely +
(wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
torque[i][2] -= vxmu2f*tz;
}
}
// set j = nlocal so that only I gets tallied
// set j = nlocal so that only I gets tallied
if (evflag) ev_tally_xyz(i,nlocal,nlocal,0,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
// restore streaming component of velocity, omega, angmom
if (shearing) {
@ -415,10 +415,10 @@ void PairLubricatePoly::compute(int eflag, int vflag)
i = ilist[ii];
itype = type[i];
radi = atom->radius[i];
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
@ -452,7 +452,7 @@ void PairLubricatePoly::init_style()
error->all(FLERR,"Pair lubricate/poly requires newton pair off");
if (comm->ghost_velocity == 0)
error->all(FLERR,
"Pair lubricate/poly requires ghost atoms store velocity");
"Pair lubricate/poly requires ghost atoms store velocity");
if (!atom->sphere_flag)
error->all(FLERR,"Pair lubricate/poly requires atom style sphere");
@ -464,7 +464,7 @@ void PairLubricatePoly::init_style()
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (radius[i] == 0.0)
if (radius[i] == 0.0)
error->one(FLERR,"Pair lubricate/poly requires extended particles");
int irequest = neighbor->request(this);
@ -482,20 +482,20 @@ void PairLubricatePoly::init_style()
// due to walls, set volume appropriately; if walls will
// move, set appropriate flag so that volume and v.f. corrections
// are re-calculated at every step.
shearing = flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = flagdeform = 1;
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using pair lubricate with inconsistent "
"fix deform remap option");
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using pair lubricate with inconsistent "
"fix deform remap option");
}
if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
}
}
@ -503,26 +503,26 @@ void PairLubricatePoly::init_style()
double vol_T;
double wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
else {
else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
@ -534,16 +534,16 @@ void PairLubricatePoly::init_style()
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
// set isotropic constants
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
@ -553,9 +553,9 @@ void PairLubricatePoly::init_style()
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
shearing = 1;
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using pair lubricate/poly with inconsistent "
"fix deform remap option");
if (((FixDeform *) modify->fix[i])->remapflag != V_REMAP)
error->all(FLERR,"Using pair lubricate/poly with inconsistent "
"fix deform remap option");
}
// set Ef = 0 since used whether shearing or not

2
src/FLD/pair_lubricate_poly.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

18
src/GPU/fix_gpu.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -45,7 +45,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->cuda)
if (lmp->cuda)
error->all(FLERR,"Cannot use fix GPU with USER-CUDA mode enabled");
if (narg < 7) error->all(FLERR,"Illegal fix GPU command");
@ -73,7 +73,7 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
_particle_split = force->numeric(arg[6]);
if (_particle_split==0 || _particle_split>1)
error->all(FLERR,"Illegal fix GPU command");
int nthreads = 1;
int threads_per_atom = -1;
if (narg == 9) {
@ -88,15 +88,15 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
if (nthreads < 1)
error->all(FLERR,"Illegal fix GPU command");
#ifndef _OPENMP
if (nthreads > 1)
error->all(FLERR,"No OpenMP support compiled in");
#endif
int gpu_flag = lmp_init_device(universe->uworld, world, first_gpu, last_gpu,
_gpu_mode, _particle_split, nthreads,
threads_per_atom);
_gpu_mode, _particle_split, nthreads,
threads_per_atom);
GPU_EXTRA::check_flag(gpu_flag,error,world);
}
@ -125,11 +125,11 @@ void FixGPU::init()
if (_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH)
if (force->pair_match("hybrid",1) != NULL ||
force->pair_match("hybrid/overlay",1) != NULL)
force->pair_match("hybrid/overlay",1) != NULL)
error->all(FLERR,"Cannot use pair hybrid with GPU neighbor builds");
if (_particle_split < 0)
if (force->pair_match("hybrid",1) != NULL ||
force->pair_match("hybrid/overlay",1) != NULL)
force->pair_match("hybrid/overlay",1) != NULL)
error->all(FLERR,"Fix GPU split must be positive for hybrid pair styles");
}
@ -140,7 +140,7 @@ void FixGPU::setup(int vflag)
if (_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH)
if (neighbor->exclude_setting()!=0)
error->all(FLERR,
"Cannot use neigh_modify exclude with GPU neighbor builds");
"Cannot use neigh_modify exclude with GPU neighbor builds");
post_force(vflag);
}

2
src/GPU/fix_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

28
src/GPU/gpu_extra.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -24,33 +24,33 @@
namespace GPU_EXTRA {
inline void check_flag(int error_flag, LAMMPS_NS::Error *error,
MPI_Comm &world) {
MPI_Comm &world) {
int all_success;
MPI_Allreduce(&error_flag, &all_success, 1, MPI_INT, MPI_MIN, world);
if (all_success != 0) {
if (all_success == -1)
error->all(FLERR,
"The package gpu command is required for gpu styles");
error->all(FLERR,
"The package gpu command is required for gpu styles");
else if (all_success == -2)
error->all(FLERR,
"Could not find/initialize a specified accelerator device");
error->all(FLERR,
"Could not find/initialize a specified accelerator device");
else if (all_success == -3)
error->all(FLERR,"Insufficient memory on accelerator");
error->all(FLERR,"Insufficient memory on accelerator");
else if (all_success == -4)
error->all(FLERR,"GPU library not compiled for this accelerator");
error->all(FLERR,"GPU library not compiled for this accelerator");
else if (all_success == -5)
error->all(FLERR,
"Double precision is not supported on this accelerator");
error->all(FLERR,
"Double precision is not supported on this accelerator");
else if (all_success == -6)
error->all(FLERR,"Unable to initialize accelerator for use");
error->all(FLERR,"Unable to initialize accelerator for use");
else if (all_success == -7)
error->all(FLERR,
error->all(FLERR,
"Accelerator sharing is not currently supported on system");
else if (all_success == -8)
error->all(FLERR,
error->all(FLERR,
"GPU particle split must be set to 1 for this pair style.");
else
error->all(FLERR,"Unknown error in GPU library");
error->all(FLERR,"Unknown error in GPU library");
}
};

152
src/GPU/pair_buck_coul_cut_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,40 +38,40 @@
// External functions from cuda library for atom decomposition
int buckc_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_buck1, double **host_buck2, double **host_a,
double **host_c, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double **host_cut_coulsq, double *host_special_coul,
const double qqrd2e);
double **host_buck1, double **host_buck2, double **host_a,
double **host_c, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double **host_cut_coulsq, double *host_special_coul,
const double qqrd2e);
void buckc_gpu_clear();
int ** buckc_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
void buckc_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double buckc_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
gpu_mode(GPU_FORCE)
PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -89,30 +89,30 @@ void PairBuckCoulCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buckc_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success,
atom->q, domain->boxlo, domain->prd);
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success,
atom->q, domain->boxlo, domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buckc_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -130,9 +130,9 @@ void PairBuckCoulCutGPU::compute(int eflag, int vflag)
void PairBuckCoulCutGPU::init_style()
{
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,
"Cannot use newton pair with buck/coul/cut/gpu pair style");
"Cannot use newton pair with buck/coul/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
@ -154,18 +154,18 @@ void PairBuckCoulCutGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = buckc_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e);
int success = buckc_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
}
}
}
/* ---------------------------------------------------------------------- */
@ -179,8 +179,8 @@ double PairBuckCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh) {
int *ilist, int *numneigh,
int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair;
double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
@ -188,7 +188,7 @@ void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *jlist;
evdwl = ecoul = 0.0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
@ -196,7 +196,7 @@ void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double qqrd2e = force->qqrd2e;
// loop over neighbors of my atoms
for (ii = start; ii < inum; ii++) {
@ -222,37 +222,37 @@ void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]/r;
else forcecoul = 0.0;
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]/r;
else forcecoul = 0.0;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
fpair = (factor_coul*forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]/r;
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_buck_coul_cut_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

158
src/GPU/pair_buck_coul_long_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -47,40 +47,40 @@
// External functions from cuda library for atom decomposition
int buckcl_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_buck1, double **host_buck2, double **host_a,
double **host_c, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
double **host_buck1, double **host_buck2, double **host_a,
double **host_c, double **offset, double *special_lj,
const int inum, const int nall, const int max_nbors,
const int maxspecial, const double cell_size,
int &gpu_mode, FILE *screen, double **host_cut_ljsq,
double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
void buckcl_gpu_clear();
int** buckcl_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
void buckcl_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double buckcl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
PairBuckCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -98,30 +98,30 @@ void PairBuckCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buckcl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buckcl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -141,10 +141,10 @@ void PairBuckCoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,
"Pair style buck/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
"Pair style buck/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
error->all(FLERR,
"Cannot use newton pair with buck/coul/long/gpu pair style");
"Cannot use newton pair with buck/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
@ -174,12 +174,12 @@ void PairBuckCoulLongGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = buckcl_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e,
g_ewald);
int success = buckcl_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e,
g_ewald);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -200,8 +200,8 @@ double PairBuckCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@ -246,44 +246,44 @@ void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (rsq < cut_coulsq) {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_buck_coul_long_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

100
src/GPU/pair_buck_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,24 +38,24 @@
// External functions from cuda library for atom decomposition
int buck_gpu_init(const int ntypes, double **cutsq, double **host_rhoinv,
double **host_buck1, double **host_buck2,
double **host_a, double **host_c,
double **offset, double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
double **host_buck1, double **host_buck2,
double **host_a, double **host_c,
double **offset, double *special_lj, const int inum,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void buck_gpu_clear();
int ** buck_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success);
void buck_gpu_compute(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double buck_gpu_bytes();
using namespace LAMMPS_NS;
@ -66,7 +66,7 @@ PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -84,28 +84,28 @@ void PairBuckGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = buck_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
buck_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -123,7 +123,7 @@ void PairBuckGPU::compute(int eflag, int vflag)
void PairBuckGPU::init_style()
{
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with buck/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -146,10 +146,10 @@ void PairBuckGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = buck_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
int success = buck_gpu_init(atom->ntypes+1, cutsq, rhoinv, buck1, buck2,
a, c, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -169,8 +169,8 @@ double PairBuckGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcebuck,factor_lj;
@ -205,24 +205,24 @@ void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
fpair = factor_lj*forcebuck*r2inv;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
fpair = factor_lj*forcebuck*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (eflag) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_buck_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

154
src/GPU/pair_coul_long_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -47,36 +47,36 @@
// External functions from cuda library for atom decomposition
int cl_gpu_init(const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double host_cut_coulsq, double *host_special_coul,
const double qqrd2e, const double g_ewald);
void cl_gpu_clear();
int ** cl_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
void cl_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double cl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
PairCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -94,30 +94,30 @@ void PairCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = cl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
cl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -139,7 +139,7 @@ void PairCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/long/gpu requires atom attribute q");
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -160,9 +160,9 @@ void PairCoulLongGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = cl_gpu_init(atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen, cut_coulsq,
force->special_coul, force->qqrd2e, g_ewald);
int success = cl_gpu_init(atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen, cut_coulsq,
force->special_coul, force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success,error,world);
@ -184,8 +184,8 @@ double PairCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@ -230,49 +230,49 @@ void PairCoulLongGPU::cpu_compute(int start, int inum, int eflag,
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
fpair = forcecoul * r2inv;
fpair = forcecoul * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
}
if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,0.0,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_coul_long_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

24
src/GPU/pair_eam_alloy_gpu.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -96,9 +96,9 @@ void PairEAMAlloyGPU::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
count++;
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
count++;
}
}
}
@ -147,7 +147,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@ -164,7 +164,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@ -177,7 +177,7 @@ void PairEAMAlloyGPU::read_file(char *filename)
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
"pair:z2r");
"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@ -226,7 +226,7 @@ void PairEAMAlloyGPU::file2array()
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@ -307,12 +307,12 @@ void PairEAMAlloyGPU::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
type2z2r[i][j] = 0;
continue;
type2z2r[i][j] = 0;
continue;
}
if (irow < icol) {
irow = map[j];
icol = map[i];
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;

2
src/GPU/pair_eam_alloy_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

28
src/GPU/pair_eam_fs_gpu.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -96,9 +96,9 @@ void PairEAMFSGPU::coeff(int narg, char **arg)
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,fs->mass[map[i]]);
count++;
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,fs->mass[map[i]]);
count++;
}
}
}
@ -147,7 +147,7 @@ void PairEAMFSGPU::read_file(char *filename)
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in EAM potential file");
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
@ -164,7 +164,7 @@ void PairEAMFSGPU::read_file(char *filename)
if (me == 0) {
fgets(line,MAXLINE,fptr);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
@ -175,11 +175,11 @@ void PairEAMFSGPU::read_file(char *filename)
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,
"pair:frho");
"pair:frho");
memory->create(file->rhor,file->nelements,file->nelements,
file->nr+1,"pair:rhor");
file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,
file->nr+1,"pair:z2r");
file->nr+1,"pair:z2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
@ -231,7 +231,7 @@ void PairEAMFSGPU::file2array()
// allocate frho arrays
// nfrho = # of fs elements + 1 for zero array
nfrho = fs->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
@ -316,12 +316,12 @@ void PairEAMFSGPU::file2array()
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) {
type2z2r[i][j] = 0;
continue;
type2z2r[i][j] = 0;
continue;
}
if (irow < icol) {
irow = map[j];
icol = map[i];
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;

2
src/GPU/pair_eam_fs_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

94
src/GPU/pair_eam_gpu.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -38,30 +38,30 @@ using namespace LAMMPS_NS;
// External functions from cuda library for atom decomposition
int eam_gpu_init(const int ntypes, double host_cutforcesq,
int **host_type2rhor, int **host_type2z2r,
int **host_type2rhor, int **host_type2z2r,
int *host_type2frho, double ***host_rhor_spline,
double ***host_z2r_spline, double ***host_frho_spline,
double ***host_z2r_spline, double ***host_frho_spline,
double rdr, double rdrho, int nrhor, int nrho, int nz2r,
int nfrho, int nr, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
int &fp_size);
int nfrho, int nr, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
int &fp_size);
void eam_gpu_clear();
int** eam_gpu_compute_n(const int ago, const int inum_full, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial, int **special,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, int **ilist,
int **jnum, const double cpu_time, bool &success,
int &inum, void **fp_ptr);
void eam_gpu_compute(const int ago, const int inum_full, const int nlocal,
const int nall,double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, void **fp_ptr);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial, int **special,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, int **ilist,
int **jnum, const double cpu_time, bool &success,
int &inum, void **fp_ptr);
void eam_gpu_compute(const int ago, const int inum_full, const int nlocal,
const int nall,double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, void **fp_ptr);
void eam_gpu_compute_force(int *ilist, const bool eflag, const bool vflag,
const bool eatom, const bool vatom);
const bool eatom, const bool vatom);
double eam_gpu_bytes();
/* ---------------------------------------------------------------------- */
@ -70,7 +70,7 @@ PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -100,44 +100,44 @@ void PairEAMGPU::compute(int eflag, int vflag)
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
// compute density on each atom on GPU
int nall = atom->nlocal + atom->nghost;
int nall = atom->nlocal + atom->nghost;
int inum, host_start, inum_dev;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = eam_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, inum_dev, &fp_pinned);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, inum_dev, &fp_pinned);
} else { // gpu_mode == GPU_FORCE
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
eam_gpu_compute(neighbor->ago, inum, nlocal, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, &fp_pinned);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, &fp_pinned);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
// communicate derivative of embedding function
comm->forward_comm_pair(this);
// compute forces on each atom on GPU
if (gpu_mode != GPU_FORCE)
if (gpu_mode != GPU_FORCE)
eam_gpu_compute_force(NULL, eflag, vflag, eflag_atom, vflag_atom);
else
eam_gpu_compute_force(ilist, eflag, vflag, eflag_atom, vflag_atom);
@ -149,14 +149,14 @@ void PairEAMGPU::compute(int eflag, int vflag)
void PairEAMGPU::init_style()
{
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with eam/gpu pair style");
// convert read-in file(s) to arrays and spline them
file2array();
array2spline();
// Repeat cutsq calculation because done after call to init_style
double maxcut = -1.0;
double cut;
@ -173,18 +173,18 @@ void PairEAMGPU::init_style()
}
}
double cell_size = sqrt(maxcut) + neighbor->skin;
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int fp_size;
int success = eam_gpu_init(atom->ntypes+1, cutforcesq, type2rhor, type2z2r,
type2frho, rhor_spline, z2r_spline, frho_spline,
rdr, rdrho, nrhor, nrho, nz2r, nfrho, nr,
atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen, fp_size);
type2frho, rhor_spline, z2r_spline, frho_spline,
rdr, rdrho, nrhor, nrho, nz2r, nfrho, nr,
atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen, fp_size);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
@ -199,8 +199,8 @@ void PairEAMGPU::init_style()
/* ---------------------------------------------------------------------- */
int PairEAMGPU::pack_comm(int n, int *list, double *buf, int pbc_flag,
int *pbc)
int PairEAMGPU::pack_comm(int n, int *list, double *buf, int pbc_flag,
int *pbc)
{
int i,j,m;

4
src/GPU/pair_eam_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -44,7 +44,7 @@ class PairEAMGPU : public PairEAM {
double cpu_time;
int *gpulist;
void *fp_pinned;
bool fp_single;
bool fp_single;
};
}

170
src/GPU/pair_gayberne_gpu.cpp
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -40,26 +40,26 @@
// External functions from cuda library for atom decomposition
int gb_gpu_init(const int ntypes, const double gamma, const double upsilon,
const double mu, double **shape, double **well, double **cutsq,
double **sigma, double **epsilon, double *host_lshape,
int **form, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
const double mu, double **shape, double **well, double **cutsq,
double **sigma, double **epsilon, double *host_lshape,
int **form, double **host_lj1, double **host_lj2,
double **host_lj3, double **host_lj4, double **offset,
double *special_lj, const int nlocal, const int nall,
const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void gb_gpu_clear();
int ** gb_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial, int **special,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double **host_quat);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial, int **special,
const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double **host_quat);
int * gb_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double **host_quat);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double **host_quat);
double gb_gpu_bytes();
using namespace LAMMPS_NS;
@ -72,11 +72,11 @@ PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
gpu_mode(GPU_FORCE)
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
if (!avec)
error->all(FLERR,"Pair gayberne/gpu requires atom style ellipsoid");
quat_nmax = 0;
quat = NULL;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -101,7 +101,7 @@ void PairGayBerneGPU::compute(int eflag, int vflag)
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (nall > quat_nmax) {
quat_nmax = static_cast<int>(1.1 * nall);
@ -122,19 +122,19 @@ void PairGayBerneGPU::compute(int eflag, int vflag)
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = gb_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, quat);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, quat);
} else {
inum = list->inum;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ilist = gb_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
list->ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start,
cpu_time, success, quat);
list->ilist, numneigh, firstneigh, eflag, vflag,
eflag_atom, vflag_atom, host_start,
cpu_time, success, quat);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -152,7 +152,7 @@ void PairGayBerneGPU::compute(int eflag, int vflag)
void PairGayBerneGPU::init_style()
{
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with gayberne/gpu pair style");
if (!atom->ellipsoid_flag)
error->all(FLERR,"Pair gayberne/gpu requires atom style ellipsoid");
@ -169,7 +169,7 @@ void PairGayBerneGPU::init_style()
shape2[i][0] = shape1[i][0]*shape1[i][0];
shape2[i][1] = shape1[i][1]*shape1[i][1];
shape2[i][2] = shape1[i][2]*shape1[i][2];
lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
lshape[i] = (shape1[i][0]*shape1[i][1]+shape1[i][2]*shape1[i][2]) *
sqrt(shape1[i][0]*shape1[i][1]);
}
@ -194,11 +194,11 @@ void PairGayBerneGPU::init_style()
int maxspecial=0;
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,
shape2, well, cutsq, sigma, epsilon, lshape, form,
lj1, lj2, lj3, lj4, offset, force->special_lj,
atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen);
int success = gb_gpu_init(atom->ntypes+1, gamma, upsilon, mu,
shape2, well, cutsq, sigma, epsilon, lshape, form,
lj1, lj2, lj3, lj4, offset, force->special_lj,
atom->nlocal, atom->nlocal+atom->nghost, 300,
maxspecial, cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -221,7 +221,7 @@ double PairGayBerneGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
@ -273,68 +273,68 @@ void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, int vflag,
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
switch (form[itype][jtype]) {
case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
if (eflag) one_eng =
r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
fforce[0] = r12[0]*forcelj;
fforce[1] = r12[1]*forcelj;
fforce[2] = r12[2]*forcelj;
ttor[0] = ttor[1] = ttor[2] = 0.0;
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
case SPHERE_ELLIPSE:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_lj(j,i,a2,b2,g2,r12,rsq,fforce,rtor);
ttor[0] = ttor[1] = ttor[2] = 0.0;
break;
case ELLIPSE_SPHERE:
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
one_eng = gayberne_lj(i,j,a1,b1,g1,r12,rsq,fforce,ttor);
rtor[0] = rtor[1] = rtor[2] = 0.0;
break;
default:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
default:
jquat = bonus[ellipsoid[j]].quat;
MathExtra::quat_to_mat_trans(jquat,a2);
MathExtra::diag_times3(well[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,b2);
MathExtra::diag_times3(shape2[jtype],a2,temp);
MathExtra::transpose_times3(a2,temp,g2);
one_eng = gayberne_analytic(i,j,a1,a2,b1,b2,g1,g2,r12,rsq,
fforce,ttor,rtor);
break;
}
fforce[0] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
fforce[1] *= factor_lj;
fforce[2] *= factor_lj;
ttor[0] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
ttor[1] *= factor_lj;
ttor[2] *= factor_lj;
f[i][0] += fforce[0];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
f[i][1] += fforce[1];
f[i][2] += fforce[2];
tor[i][0] += ttor[0];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
tor[i][1] += ttor[1];
tor[i][2] += ttor[2];
if (eflag) evdwl = factor_lj*one_eng;
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
if (evflag) ev_tally_xyz_full(i,evdwl,0.0,fforce[0],fforce[1],fforce[2],
-r12[0],-r12[1],-r12[2]);
}
}
}

2
src/GPU/pair_gayberne_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

92
src/GPU/pair_lj96_cut_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void lj96_gpu_clear();
int ** lj96_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
void lj96_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double lj96_gpu_bytes();
using namespace LAMMPS_NS;
@ -65,7 +65,7 @@ PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_FOR
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -83,28 +83,28 @@ void PairLJ96CutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = lj96_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
lj96_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -124,7 +124,7 @@ void PairLJ96CutGPU::init_style()
{
cut_respa = NULL;
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj96/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -148,9 +148,9 @@ void PairLJ96CutGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -171,7 +171,7 @@ double PairLJ96CutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@ -206,23 +206,23 @@ void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r3inv = sqrt(r6inv);
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r3inv = sqrt(r6inv);
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj96_cut_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

228
src/GPU/pair_lj_charmm_coul_long_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -47,42 +47,42 @@
// External functions from cuda library for atom decomposition
int crml_gpu_init(const int ntypes, double cut_bothsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double cut_lj_innersq,
const double denom_lj, double **epsilon, double **sigma,
const bool mix_arithmetic);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald, const double cut_lj_innersq,
const double denom_lj, double **epsilon, double **sigma,
const bool mix_arithmetic);
void crml_gpu_clear();
int ** crml_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
void crml_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double crml_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
PairLJCharmmCoulLong(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -100,30 +100,30 @@ void PairLJCharmmCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = crml_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
crml_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -145,7 +145,7 @@ void PairLJCharmmCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/charmm/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/charmm/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -162,7 +162,7 @@ void PairLJCharmmCoulLongGPU::init_style()
cut_coulsq = cut_coul * cut_coul;
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
(cut_ljsq-cut_lj_innersq);
double cell_size = sqrt(cut_bothsq) + neighbor->skin;
@ -185,18 +185,18 @@ void PairLJCharmmCoulLongGPU::init_style()
for (int i = 1; i < atom->ntypes + 1; i++)
for (int j = i + 1; j < atom->ntypes + 1; j++) {
if (epsilon[i][j] != sqrt(epsilon[i][i] * epsilon[j][j]))
arithmetic = false;
arithmetic = false;
if (sigma[i][j] != 0.5 * (sigma[i][i] + sigma[j][j]))
arithmetic = false;
arithmetic = false;
}
int success = crml_gpu_init(atom->ntypes+1, cut_bothsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e,
g_ewald, cut_lj_innersq,denom_lj,epsilon,sigma,
arithmetic);
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul, force->qqrd2e,
g_ewald, cut_lj_innersq,denom_lj,epsilon,sigma,
arithmetic);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -217,8 +217,8 @@ double PairLJCharmmCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist,
int *numneigh, int **firstneigh)
int vflag, int *ilist,
int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@ -263,77 +263,77 @@ void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag,
rsq = delx*delx + dely*dely + delz*delz;
if (rsq < cut_bothsq) {
r2inv = 1.0/rsq;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
if (rsq < cut_ljsq) {
r6inv = r2inv*r2inv*r2inv;
jtype = type[j];
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
switch2 = 12.0*rsq * (cut_ljsq-rsq) *
(rsq-cut_lj_innersq) / denom_lj;
philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
forcelj = forcelj*switch1 + philj*switch2;
}
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (rsq < cut_ljsq) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
if (rsq > cut_lj_innersq) {
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
evdwl *= switch1;
}
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_charmm_coul_long_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

144
src/GPU/pair_lj_class2_coul_long_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -47,39 +47,39 @@
// External functions from cuda library for atom decomposition
int c2cl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
void c2cl_gpu_clear();
int ** c2cl_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
void c2cl_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double c2cl_gpu_bytes();
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
PairLJClass2CoulLong(lmp), gpu_mode(GPU_FORCE)
{
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -97,30 +97,30 @@ void PairLJClass2CoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = c2cl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
c2cl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -140,7 +140,7 @@ void PairLJClass2CoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/class2/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/class2/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -196,8 +196,8 @@ double PairLJClass2CoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@ -241,45 +241,45 @@ void PairLJClass2CoulLongGPU::cpu_compute(int start, int inum, int eflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
rinv = sqrt(r2inv);
r3inv = r2inv*rinv;
r6inv = r3inv*r3inv;
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (eflag) {
if (rsq < cut_coulsq) {
ecoul = prefactor*erfc;
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_class2_coul_long_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

92
src/GPU/pair_lj_class2_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int lj96_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void lj96_gpu_clear();
int ** lj96_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
void lj96_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double lj96_gpu_bytes();
using namespace LAMMPS_NS;
@ -64,7 +64,7 @@ using namespace LAMMPS_NS;
PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_FORCE)
{
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -82,28 +82,28 @@ void PairLJClass2GPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = lj96_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
lj96_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -121,7 +121,7 @@ void PairLJClass2GPU::compute(int eflag, int vflag)
void PairLJClass2GPU::init_style()
{
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/class2/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -145,9 +145,9 @@ void PairLJClass2GPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = lj96_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -168,7 +168,7 @@ double PairLJClass2GPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@ -203,23 +203,23 @@ void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r3inv = sqrt(r6inv);
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
r3inv = sqrt(r6inv);
forcelj = r6inv * (lj1[itype][jtype]*r3inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r3inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_class2_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

116
src/GPU/pair_lj_cut_coul_cut_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,28 +38,28 @@
// External functions from cuda library for atom decomposition
int ljc_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double **host_cut_coulsq,
double *host_special_coul, const double qqrd2e);
void ljc_gpu_clear();
int ** ljc_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
void ljc_gpu_compute(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
const int nall, double **host_x, int *host_type,
int *ilist, int *numj, int **firstneigh,
const bool eflag, const bool vflag, const bool eatom,
const bool eflag, const bool vflag, const bool eatom,
const bool vatom, int &host_start, const double cpu_time,
bool &success, double *host_q, const int nlocal,
double *boxlo, double *prd);
double *boxlo, double *prd);
double ljc_gpu_bytes();
using namespace LAMMPS_NS;
@ -70,7 +70,7 @@ PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), g
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -88,30 +88,30 @@ void PairLJCutCoulCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljc_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljc_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -132,7 +132,7 @@ void PairLJCutCoulCutGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/coul/cut/gpu requires atom attribute q");
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/coul/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -156,10 +156,10 @@ void PairLJCutCoulCutGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = ljc_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq,
force->special_coul, force->qqrd2e);
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq,
force->special_coul, force->qqrd2e);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -180,8 +180,8 @@ double PairLJCutCoulCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh,
int **firstneigh)
int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@ -223,35 +223,35 @@ void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_coulsq[itype][jtype])
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (eflag) {
if (rsq < cut_coulsq[itype][jtype])
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_cut_coul_cut_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

178
src/GPU/pair_lj_cut_coul_long_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -47,28 +47,28 @@
// External functions from cuda library for atom decomposition
int ljcl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen,
double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
void ljcl_gpu_clear();
int ** ljcl_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag,
int **nspecial, int **special, const bool eflag,
const bool vflag, const bool eatom, const bool vatom,
int &host_start, int **ilist, int **jnum,
const double cpu_time, bool &success, double *host_q,
double *boxlo, double *prd);
void ljcl_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double ljcl_gpu_bytes();
using namespace LAMMPS_NS;
@ -80,7 +80,7 @@ PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -98,30 +98,30 @@ void PairLJCutCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljcl_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljcl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -143,7 +143,7 @@ void PairLJCutCoulLongGPU::init_style()
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -203,8 +203,8 @@ double PairLJCutCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongGPU::cpu_compute(int start, int inum, int eflag,
int vflag, int *ilist, int *numneigh,
int **firstneigh)
int vflag, int *ilist, int *numneigh,
int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype,itable;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
@ -249,64 +249,64 @@ void PairLJCutCoulLongGPU::cpu_compute(int start, int inum, int eflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor = qqrd2e * qtmp*q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_cut_coul_long_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

94
src/GPU/pair_lj_cut_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,23 +38,23 @@
// External functions from cuda library for atom decomposition
int ljl_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double *special_lj, const int nlocal,
const int nall, const int max_nbors, const int maxspecial,
const double cell_size, int &gpu_mode, FILE *screen);
void ljl_gpu_clear();
int ** ljl_gpu_compute_n(const int ago, const int inum,
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
void ljl_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
const int nall, double **host_x, int *host_type,
double *sublo, double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
void ljl_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double ljl_gpu_bytes();
using namespace LAMMPS_NS;
@ -65,7 +65,7 @@ PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -83,28 +83,28 @@ void PairLJCutGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = ljl_gpu_compute_n(neighbor->ago, inum, nall,
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
atom->x, atom->type, domain->sublo,
domain->subhi, atom->tag, atom->nspecial,
atom->special, eflag, vflag, eflag_atom,
vflag_atom, host_start,
&ilist, &numneigh, cpu_time, success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
ljl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -124,7 +124,7 @@ void PairLJCutGPU::init_style()
{
cut_respa = NULL;
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/cut/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -148,9 +148,9 @@ void PairLJCutGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = ljl_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -170,8 +170,8 @@ double PairLJCutGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh) {
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r2inv,r6inv,forcelj,factor_lj;
@ -205,22 +205,22 @@ void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_cut_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

100
src/GPU/pair_lj_expand_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -38,24 +38,24 @@
// External functions from cuda library for atom decomposition
int lje_gpu_init(const int ntypes, double **cutsq, double **host_lj1,
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double **shift, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen);
double **host_lj2, double **host_lj3, double **host_lj4,
double **offset, double **shift, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen);
void lje_gpu_clear();
int ** lje_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum,
const double cpu_time, bool &success);
void lje_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success);
double lje_gpu_bytes();
using namespace LAMMPS_NS;
@ -66,7 +66,7 @@ PairLJExpandGPU::PairLJExpandGPU(LAMMPS *lmp) : PairLJExpand(lmp), gpu_mode(GPU_
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -84,28 +84,28 @@ void PairLJExpandGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = lje_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
lje_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -123,7 +123,7 @@ void PairLJExpandGPU::compute(int eflag, int vflag)
void PairLJExpandGPU::init_style()
{
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/expand/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -147,9 +147,9 @@ void PairLJExpandGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = lje_gpu_init(atom->ntypes+1, cutsq, lj1, lj2, lj3, lj4,
offset, shift, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
offset, shift, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -170,7 +170,7 @@ double PairLJExpandGPU::memory_usage()
/* ---------------------------------------------------------------------- */
void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, int vflag,
int *ilist, int *numneigh, int **firstneigh)
int *ilist, int *numneigh, int **firstneigh)
{
int i,j,ii,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
@ -206,25 +206,25 @@ void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, int vflag,
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
rshift = r - shift[itype][jtype];
rshiftsq = rshift*rshift;
r2inv = 1.0/rshiftsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj/rshift/r;
r = sqrt(rsq);
rshift = r - shift[itype][jtype];
rshiftsq = rshift*rshift;
r2inv = 1.0/rshiftsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj/rshift/r;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (eflag) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
}
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
if (evflag) ev_tally_full(i,evdwl,0.0,fpair,delx,dely,delz);
}
}
}

2
src/GPU/pair_lj_expand_gpu.h
View File

@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.

174
src/GPU/pair_lj_sdk_coul_long_gpu.cpp
View File

@ -2,12 +2,12 @@
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
@ -47,28 +47,28 @@
// External functions from cuda library for atom decomposition
int cmml_gpu_init(const int ntypes, double **cutsq, int **lj_type,
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
double **host_lj1, double **host_lj2, double **host_lj3,
double **host_lj4, double **offset, double *special_lj,
const int nlocal, const int nall, const int max_nbors,
const int maxspecial, const double cell_size, int &gpu_mode,
FILE *screen, double **host_cut_ljsq, double host_cut_coulsq,
double *host_special_coul, const double qqrd2e,
const double g_ewald);
void cmml_gpu_clear();
int ** cmml_gpu_compute_n(const int ago, const int inum, const int nall,
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
double **host_x, int *host_type, double *sublo,
double *subhi, int *tag, int **nspecial,
int **special, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
int **ilist, int **jnum, const double cpu_time,
bool &success, double *host_q, double *boxlo,
double *prd);
void cmml_gpu_compute(const int ago, const int inum, const int nall,
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double **host_x, int *host_type, int *ilist, int *numj,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, double *host_q,
const int nlocal, double *boxlo, double *prd);
double cmml_gpu_bytes();
#include "lj_sdk_common.h"
@ -83,7 +83,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
{
respa_enable = 0;
cpu_time = 0.0;
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
}
/* ----------------------------------------------------------------------
@ -101,30 +101,30 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag)
{
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int nall = atom->nlocal + atom->nghost;
int inum, host_start;
bool success = true;
int *ilist, *numneigh, **firstneigh;
int *ilist, *numneigh, **firstneigh;
if (gpu_mode != GPU_FORCE) {
inum = atom->nlocal;
firstneigh = cmml_gpu_compute_n(neighbor->ago, inum, nall, atom->x,
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
atom->type, domain->sublo, domain->subhi,
atom->tag, atom->nspecial, atom->special,
eflag, vflag, eflag_atom, vflag_atom,
host_start, &ilist, &numneigh, cpu_time,
success, atom->q, domain->boxlo,
domain->prd);
} else {
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
cmml_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type,
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
ilist, numneigh, firstneigh, eflag, vflag, eflag_atom,
vflag_atom, host_start, cpu_time, success, atom->q,
atom->nlocal, domain->boxlo, domain->prd);
}
if (!success)
error->one(FLERR,"Insufficient memory on accelerator");
@ -147,7 +147,7 @@ void PairLJSDKCoulLongGPU::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/sdk/coul/long/gpu requires atom attribute q");
if (force->newton_pair)
if (force->newton_pair)
error->all(FLERR,"Cannot use newton pair with lj/sdk/coul/long/gpu pair style");
// Repeat cutsq calculation because done after call to init_style
@ -183,11 +183,11 @@ void PairLJSDKCoulLongGPU::init_style()
if (atom->molecular)
maxspecial=atom->maxspecial;
int success = cmml_gpu_init(atom->ntypes+1, cutsq, lj_type, lj1, lj2, lj3,
lj4, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul,
force->qqrd2e, g_ewald);
lj4, offset, force->special_lj, atom->nlocal,
atom->nlocal+atom->nghost, 300, maxspecial,
cell_size, gpu_mode, screen, cut_ljsq,
cut_coulsq, force->special_coul,
force->qqrd2e, g_ewald);
GPU_EXTRA::check_flag(success,error,world);
if (gpu_mode == GPU_FORCE) {
@ -208,7 +208,7 @@ double PairLJSDKCoulLongGPU::memory_usage()
/* ---------------------------------------------------------------------- */
template <int EVFLAG, int EFLAG>
void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
int *numneigh, int **firstneigh)
int *numneigh, int **firstneigh)
{
int i,j,ii,jj;
double qtmp,xtmp,ytmp,ztmp;
@ -255,11 +255,11 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
double fpair = 0.0;
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
const int ljt = lj_type[itype][jtype];
r2inv = 1.0/rsq;
const int ljt = lj_type[itype][jtype];
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
const double r = sqrt(rsq);
const double grij = g_ewald * r;
const double expm2 = exp(-grij*grij);
@ -272,7 +272,7 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
} else {
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
int itable = rsq_lookup.i & ncoulmask;
@ -291,56 +291,56 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist,
forcecoul -= (1.0-factor_coul)*prefactor;
if (EFLAG) ecoul -= (1.0-factor_coul)*prefactor;
}
}
} else {
forcecoul = 0.0;
ecoul = 0.0;
}
}
} else {
forcecoul = 0.0;
ecoul = 0.0;
}
if (rsq < cut_ljsq[itype][jtype]) {
if (rsq < cut_ljsq[itype][jtype]) {
if (ljt == LJ12_4) {
const double r4inv=r2inv*r2inv;
forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (ljt == LJ12_4) {
const double r4inv=r2inv*r2inv;
forcelj = r4inv*(lj1[itype][jtype]*r4inv*r4inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
} else if (ljt == LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
forcelj = r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
if (EFLAG)
evdwl = r4inv*(lj3[itype][jtype]*r4inv*r4inv
- lj4[itype][jtype]) - offset[itype][jtype];
} else if (ljt == LJ12_6) {
const double r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else if (ljt == LJ9_6) {
const double r3inv = r2inv*sqrt(r2inv);
const double r6inv = r3inv*r3inv;
forcelj = r6inv*(lj1[itype][jtype]*r3inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv*(lj3[itype][jtype]*r3inv
- lj4[itype][jtype]) - offset[itype][jtype];
if (EFLAG) evdwl *= factor_lj;
} else if (ljt == LJ12_6) {
const double r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv*(lj1[itype][jtype]*r6inv
- lj2[itype][jtype]);
if (EFLAG)
evdwl = r6inv*(lj3[itype][jtype]*r6inv
- lj4[itype][jtype]) - offset[itype][jtype];
}
} else {
forcelj=0.0;
evdwl = 0.0;
}
if (EFLAG) evdwl *= factor_lj;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
} else {
forcelj=0.0;
evdwl = 0.0;
}
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
if (EVFLAG) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
fxtmp += delx*fpair;
fytmp += dely*fpair;
fztmp += delz*fpair;
if (EVFLAG) ev_tally_full(i,evdwl,ecoul,fpair,delx,dely,delz);
}
}
f[i][0] += fxtmp;

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