forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8497 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
parent
5e52200ad3
commit
912cfaca75
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@ -136,7 +136,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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map_style = 0;
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map_tag_max = 0;
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map_nhash = 0;
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smax = 0;
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sametag = NULL;
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map_array = NULL;
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@ -599,11 +599,11 @@ void Atom::data_atoms(int n, char *buf)
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}
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if (imageflag)
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imagedata =
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imagedata =
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(((tagint) atoi(values[iptr+2]) + IMGMAX & IMGMASK) << IMG2BITS) |
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(((tagint) atoi(values[iptr+1]) + IMGMAX & IMGMASK) << IMGBITS) |
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(atoi(values[iptr]) + IMGMAX & IMGMASK);
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else imagedata = ((tagint) IMGMAX << IMG2BITS) |
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else imagedata = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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xdata[0] = atof(values[xptr]);
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@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -46,7 +46,7 @@ AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp, int narg, char **arg) :
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by DELTA
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n > 0 allocates arrays to size n
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecAtomic::grow(int n)
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@ -66,7 +66,7 @@ void AtomVecAtomic::grow(int n)
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f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
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}
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@ -99,14 +99,14 @@ void AtomVecAtomic::copy(int i, int j, int delflag)
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v[j][2] = v[i][2];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz;
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@ -142,7 +142,7 @@ int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz,dvx,dvy,dvz;
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@ -170,32 +170,32 @@ int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
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}
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if (!deform_vremap) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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} else {
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dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
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dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
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dvz = pbc[2]*h_rate[2];
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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}
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}
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}
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@ -269,7 +269,7 @@ void AtomVecAtomic::unpack_reverse(int n, int *list, double *buf)
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_border(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz;
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@ -311,7 +311,7 @@ int AtomVecAtomic::pack_border(int n, int *list, double *buf,
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz,dvx,dvy,dvz;
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@ -342,38 +342,38 @@ int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
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}
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if (!deform_vremap) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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} else {
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dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
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dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
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dvz = pbc[2]*h_rate[2];
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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}
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}
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}
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@ -423,7 +423,7 @@ void AtomVecAtomic::unpack_border_vel(int n, int first, double *buf)
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/* ----------------------------------------------------------------------
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pack data for atom I for sending to another proc
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xyz must be 1st 3 values, so comm::exchange() can test on them
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xyz must be 1st 3 values, so comm::exchange() can test on them
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------------------------------------------------------------------------- */
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int AtomVecAtomic::pack_exchange(int i, double *buf)
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@ -441,7 +441,7 @@ int AtomVecAtomic::pack_exchange(int i, double *buf)
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*((tagint *) &buf[m++]) = image[i];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
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buf[0] = m;
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@ -468,9 +468,9 @@ int AtomVecAtomic::unpack_exchange(double *buf)
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image[nlocal] = *((tagint *) &buf[m++]);
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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m += modify->fix[atom->extra_grow[iextra]]->
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unpack_exchange(nlocal,&buf[m]);
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unpack_exchange(nlocal,&buf[m]);
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atom->nlocal++;
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return m;
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@ -489,9 +489,9 @@ int AtomVecAtomic::size_restart()
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int n = 11 * nlocal;
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if (atom->nextra_restart)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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for (i = 0; i < nlocal; i++)
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n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
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n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
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return n;
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}
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@ -499,7 +499,7 @@ int AtomVecAtomic::size_restart()
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/* ----------------------------------------------------------------------
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pack atom I's data for restart file including extra quantities
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xyz must be 1st 3 values, so that read_restart can test on them
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molecular types may be negative, but write as positive
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molecular types may be negative, but write as positive
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------------------------------------------------------------------------- */
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int AtomVecAtomic::pack_restart(int i, double *buf)
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@ -517,7 +517,7 @@ int AtomVecAtomic::pack_restart(int i, double *buf)
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buf[m++] = v[i][2];
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if (atom->nextra_restart)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
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m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
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buf[0] = m;
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@ -575,7 +575,7 @@ void AtomVecAtomic::create_atom(int itype, double *coord)
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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mask[nlocal] = 1;
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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@ -617,7 +617,7 @@ void AtomVecAtomic::data_atom(double *coord, tagint imagetmp, char **values)
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}
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/* ----------------------------------------------------------------------
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return # of bytes of allocated memory
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return # of bytes of allocated memory
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------------------------------------------------------------------------- */
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bigint AtomVecAtomic::memory_usage()
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@ -624,7 +624,7 @@ void AtomVecCharge::create_atom(int itype, double *coord)
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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mask[nlocal] = 1;
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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@ -1094,7 +1094,7 @@ void AtomVecEllipsoid::create_atom(int itype, double *coord)
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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mask[nlocal] = 1;
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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@ -952,7 +952,7 @@ void AtomVecLine::create_atom(int itype, double *coord)
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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mask[nlocal] = 1;
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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@ -922,7 +922,7 @@ void AtomVecSphere::create_atom(int itype, double *coord)
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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mask[nlocal] = 1;
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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@ -1303,7 +1303,7 @@ void AtomVecTri::create_atom(int itype, double *coord)
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x[nlocal][1] = coord[1];
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x[nlocal][2] = coord[2];
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mask[nlocal] = 1;
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
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((tagint) IMGMAX << IMGBITS) | IMGMAX;
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v[nlocal][0] = 0.0;
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v[nlocal][1] = 0.0;
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@ -707,7 +707,7 @@ int Balance::adjust(int n, double *split)
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hi[i] = hi[i+1];
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hisum[i] = hisum[i+1];
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}
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int change = 0;
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for (int i = 1; i < n; i++)
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if (sum[i] != target[i]) {
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@ -888,11 +888,11 @@ void Balance::dumpout(bigint tstep, FILE *bfp)
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fprintf(bfp,"%d\n",nprocs);
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if (dimension == 2) fprintf(bfp,"ITEM: SQUARES\n");
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else fprintf(bfp,"ITEM: CUBES\n");
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int nx = comm->procgrid[0] + 1;
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int ny = comm->procgrid[1] + 1;
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int nz = comm->procgrid[2] + 1;
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if (dimension == 2) {
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int m = 0;
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for (int j = 0; j < comm->procgrid[1]; j++)
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@ -904,7 +904,7 @@ void Balance::dumpout(bigint tstep, FILE *bfp)
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fprintf(bfp,"%d %d %d %d %d %d\n",m+1,m+1,c1,c2,c3,c4);
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m++;
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}
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} else {
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int m = 0;
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for (int k = 0; k < comm->procgrid[2]; k++)
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@ -1000,7 +1000,7 @@ void Balance::debug_output(int idim, int m, int np, double *split)
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for (i = 0; i <= np; i++) printf(" " BIGINT_FORMAT,target[i]);
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printf("\n");
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printf(" Actual cut:");
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for (i = 0; i <= np; i++)
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for (i = 0; i <= np; i++)
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printf(" %g",boxlo[bdim[idim]] + split[i]*prd[bdim[idim]]);
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printf("\n");
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printf(" Split:");
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@ -47,7 +47,7 @@ class Balance : protected Pointers {
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char bstr[4];
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int ndim; // length of balance string bstr
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int *bdim; // XYZ for each character in bstr
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int *bdim; // XYZ for each character in bstr
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||||
bigint *count; // counts for slices in one dim
|
||||
bigint *onecount; // work vector of counts in one dim
|
||||
bigint *sum; // cummulative count for slices in one dim
|
||||
|
|
|
@ -88,7 +88,7 @@ void ComputeGyration::compute_vector()
|
|||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
|
||||
double rg[6];
|
||||
rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;
|
||||
|
||||
|
|
|
@ -179,7 +179,7 @@ void ComputeGyrationMolecule::compute_array()
|
|||
molcom();
|
||||
|
||||
for (i = 0; i < nmolecules; i++)
|
||||
for (j = 0; j < 6; j++)
|
||||
for (j = 0; j < 6; j++)
|
||||
rgt[i][j] = 0.0;
|
||||
|
||||
double **x = atom->x;
|
||||
|
@ -220,8 +220,8 @@ void ComputeGyrationMolecule::compute_array()
|
|||
MPI_Allreduce(&rgt[0][0],&array[0][0],nmolecules*6,
|
||||
MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
for (i = 0; i < nmolecules; i++)
|
||||
for (j = 0; j < 6; j++)
|
||||
for (i = 0; i < nmolecules; i++)
|
||||
for (j = 0; j < 6; j++)
|
||||
array[i][j] /= masstotal[i];
|
||||
}
|
||||
|
||||
|
|
|
@ -271,7 +271,7 @@ void CreateAtoms::add_single()
|
|||
// remap atom if requested
|
||||
|
||||
if (remapflag) {
|
||||
tagint imagetmp = ((tagint) IMGMAX << IMG2BITS) |
|
||||
tagint imagetmp = ((tagint) IMGMAX << IMG2BITS) |
|
||||
((tagint) IMGMAX << IMGBITS) | IMGMAX;
|
||||
domain->remap(xone,imagetmp);
|
||||
}
|
||||
|
|
|
@ -535,7 +535,7 @@ void Domain::box_too_small_check()
|
|||
// NOTE: if box is tiny (less than 2 * bond-length),
|
||||
// the check itself may compute bad bond lengths
|
||||
// not sure how to account for that extreme case
|
||||
|
||||
|
||||
int *num_bond = atom->num_bond;
|
||||
int **bond_atom = atom->bond_atom;
|
||||
double **x = atom->x;
|
||||
|
@ -724,7 +724,7 @@ int Domain::closest_image(int i, int j)
|
|||
double delz = xi[2] - x[j][2];
|
||||
double rsqmin = delx*delx + dely*dely + delz*delz;
|
||||
double rsq;
|
||||
|
||||
|
||||
while (sametag[j] >= 0) {
|
||||
j = sametag[j];
|
||||
delx = xi[0] - x[j][0];
|
||||
|
@ -1138,7 +1138,7 @@ void Domain::image_flip(int m, int n, int p)
|
|||
xbox -= m*ybox + n*zbox;
|
||||
|
||||
image[i] = ((zbox + (tagint) IMGMAX & IMGMASK) << IMG2BITS) |
|
||||
((ybox + (tagint) IMGMAX & IMGMASK) << IMGBITS) |
|
||||
((ybox + (tagint) IMGMAX & IMGMASK) << IMGBITS) |
|
||||
(xbox + IMGMAX & IMGMASK);
|
||||
}
|
||||
}
|
||||
|
|
|
@ -128,21 +128,21 @@ void FixAveForce::init()
|
|||
|
||||
if (xstr) {
|
||||
xvar = input->variable->find(xstr);
|
||||
if (xvar < 0)
|
||||
if (xvar < 0)
|
||||
error->all(FLERR,"Variable name for fix aveforce does not exist");
|
||||
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
|
||||
else error->all(FLERR,"Variable for fix aveforce is invalid style");
|
||||
}
|
||||
if (ystr) {
|
||||
yvar = input->variable->find(ystr);
|
||||
if (yvar < 0)
|
||||
if (yvar < 0)
|
||||
error->all(FLERR,"Variable name for fix aveforce does not exist");
|
||||
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
|
||||
else error->all(FLERR,"Variable for fix aveforce is invalid style");
|
||||
}
|
||||
if (zstr) {
|
||||
zvar = input->variable->find(zstr);
|
||||
if (zvar < 0)
|
||||
if (zvar < 0)
|
||||
error->all(FLERR,"Variable name for fix aveforce does not exist");
|
||||
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
|
||||
else error->all(FLERR,"Variable for fix aveforce is invalid style");
|
||||
|
@ -152,7 +152,7 @@ void FixAveForce::init()
|
|||
|
||||
if (iregion >= 0) {
|
||||
iregion = domain->find_region(idregion);
|
||||
if (iregion == -1)
|
||||
if (iregion == -1)
|
||||
error->all(FLERR,"Region ID for fix aveforce does not exist");
|
||||
}
|
||||
|
||||
|
|
|
@ -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.
|
||||
|
@ -52,13 +52,13 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :
|
|||
nitermax = atoi(arg[5]);
|
||||
thresh = atof(arg[6]);
|
||||
|
||||
if (nevery < 0 || nitermax <= 0 || thresh < 1.0)
|
||||
if (nevery < 0 || nitermax <= 0 || thresh < 1.0)
|
||||
error->all(FLERR,"Illegal fix balance command");
|
||||
|
||||
for (int i = 0; i < strlen(bstr); i++) {
|
||||
if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
|
||||
if (bstr[i] != 'x' && bstr[i] != 'y' && bstr[i] != 'z')
|
||||
error->all(FLERR,"Fix balance string is invalid");
|
||||
if (bstr[i] == 'z' && dimension == 2)
|
||||
if (bstr[i] == 'z' && dimension == 2)
|
||||
error->all(FLERR,"Fix balance string is invalid for 2d simulation");
|
||||
for (int j = i+1; j < strlen(bstr); j++)
|
||||
if (bstr[i] == bstr[j])
|
||||
|
@ -220,7 +220,7 @@ void FixBalance::rebalance()
|
|||
itercount = balance->dynamic();
|
||||
|
||||
// output of final result
|
||||
|
||||
|
||||
if (fp) balance->dumpout(update->ntimestep,fp);
|
||||
|
||||
// reset comm->uniform flag
|
||||
|
@ -236,7 +236,7 @@ void FixBalance::rebalance()
|
|||
// move atoms to new processors via irregular()
|
||||
// only needed if migrate_check() says an atom moves to far,
|
||||
// else allow caller's comm->exchange() to do it
|
||||
|
||||
|
||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
||||
if (irregular->migrate_check()) irregular->migrate_atoms();
|
||||
if (domain->triclinic) domain->lamda2x(atom->nlocal);
|
||||
|
|
|
@ -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.
|
||||
|
|
|
@ -438,7 +438,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
|||
// reneighboring only forced if flips will occur due to shape changes
|
||||
|
||||
if (p_flag[3] || p_flag[4] || p_flag[5]) force_reneighbor = 1;
|
||||
if (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0)
|
||||
if (domain->yz != 0.0 || domain->xz != 0.0 || domain->xy != 0.0)
|
||||
force_reneighbor = 1;
|
||||
|
||||
// convert input periods to frequencies
|
||||
|
|
|
@ -1651,7 +1651,7 @@ void FixRigid::setup_bodies()
|
|||
// then remap the xcm of each body back into simulation box if needed
|
||||
|
||||
for (ibody = 0; ibody < nbody; ibody++)
|
||||
imagebody[ibody] = ((tagint) IMGMAX << IMG2BITS) |
|
||||
imagebody[ibody] = ((tagint) IMGMAX << IMG2BITS) |
|
||||
((tagint) IMGMAX << IMGBITS) | IMGMAX;
|
||||
|
||||
pre_neighbor();
|
||||
|
@ -2003,7 +2003,7 @@ void FixRigid::readfile(int which, double *vec, double **array, int *inbody)
|
|||
FILE *fp;
|
||||
char *eof,*start,*next,*buf;
|
||||
char line[MAXLINE];
|
||||
|
||||
|
||||
if (me == 0) {
|
||||
fp = fopen(infile,"r");
|
||||
if (fp == NULL) {
|
||||
|
@ -2052,7 +2052,7 @@ void FixRigid::readfile(int which, double *vec, double **array, int *inbody)
|
|||
|
||||
if (nwords != ATTRIBUTE_PERBODY)
|
||||
error->all(FLERR,"Incorrect rigid body format in fix rigid file");
|
||||
|
||||
|
||||
// loop over lines of rigid body attributes
|
||||
// tokenize the line into values
|
||||
// id = rigid body ID
|
||||
|
@ -2062,19 +2062,19 @@ void FixRigid::readfile(int which, double *vec, double **array, int *inbody)
|
|||
|
||||
for (int i = 0; i < nchunk; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
|
||||
|
||||
values[0] = strtok(buf," \t\n\r\f");
|
||||
for (j = 1; j < nwords; j++)
|
||||
values[j] = strtok(NULL," \t\n\r\f");
|
||||
|
||||
|
||||
id = atoi(values[0]);
|
||||
if (rstyle == MOLECULE) {
|
||||
if (id <= 0 || id > maxmol)
|
||||
if (id <= 0 || id > maxmol)
|
||||
error->all(FLERR,"Invalid rigid body ID in fix rigid file");
|
||||
id = mol2body[id];
|
||||
} else id--;
|
||||
|
||||
if (id < 0 || id >= nbody)
|
||||
if (id < 0 || id >= nbody)
|
||||
error->all(FLERR,"Invalid rigid body ID in fix rigid file");
|
||||
inbody[id] = 1;
|
||||
|
||||
|
@ -2094,7 +2094,7 @@ void FixRigid::readfile(int which, double *vec, double **array, int *inbody)
|
|||
|
||||
buf = next + 1;
|
||||
}
|
||||
|
||||
|
||||
nread += nchunk;
|
||||
}
|
||||
|
||||
|
|
|
@ -126,7 +126,7 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
|
|||
} else if (mode == 'm') {
|
||||
double massone = atof(arg[next]);
|
||||
if (massone == 0.0) error->all(FLERR,"Invalid atom mass for fix shake");
|
||||
if (nmass == atom->ntypes)
|
||||
if (nmass == atom->ntypes)
|
||||
error->all(FLERR,"Too many masses for fix shake");
|
||||
mass_list[nmass++] = massone;
|
||||
|
||||
|
|
|
@ -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.
|
||||
|
|
|
@ -203,7 +203,7 @@ void Neighbor::half_bin_no_newton_ghost(NeighList *list)
|
|||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
|
||||
if (rsq <= cutneighsq[itype][jtype]) {
|
||||
if (molecular) {
|
||||
which = find_special(special[i],nspecial[i],tag[j]);
|
||||
|
|
|
@ -179,12 +179,12 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
|
|||
if (includegroup && !(mask[j] & bitmask)) continue;
|
||||
jtype = type[j];
|
||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
|
||||
if (rsq <= cutneighsq[itype][jtype]) {
|
||||
if (molecular) {
|
||||
which = find_special(special[i],nspecial[i],tag[j]);
|
||||
|
@ -201,16 +201,16 @@ void Neighbor::half_nsq_no_newton_ghost(NeighList *list)
|
|||
if (includegroup && !(mask[j] & bitmask)) continue;
|
||||
jtype = type[j];
|
||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
|
||||
if (rsq <= cutneighsq[itype][jtype]) neighptr[n++] = j;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
ilist[inum++] = i;
|
||||
firstneigh[i] = neighptr;
|
||||
numneigh[i] = n;
|
||||
|
|
|
@ -493,7 +493,7 @@ void Neighbor::init()
|
|||
lists[i]->listskip = lists[requests[i]->otherlist];
|
||||
lists[i]->copy_skip_info(requests[i]->iskip,requests[i]->ijskip);
|
||||
|
||||
} else if (requests[i]->half_from_full)
|
||||
} else if (requests[i]->half_from_full)
|
||||
lists[i]->listfull = lists[i-1];
|
||||
|
||||
else if (requests[i]->granhistory) {
|
||||
|
@ -852,7 +852,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
|
|||
else pb = &Neighbor::half_bin_no_newton_ghost;
|
||||
} else if (triclinic == 0) {
|
||||
pb = &Neighbor::half_bin_newton;
|
||||
} else if (triclinic == 1)
|
||||
} else if (triclinic == 1)
|
||||
pb = &Neighbor::half_bin_newton_tri;
|
||||
} else if (rq->newton == 1) {
|
||||
if (triclinic == 0) pb = &Neighbor::half_bin_newton;
|
||||
|
@ -966,7 +966,7 @@ void Neighbor::choose_build(int index, NeighRequest *rq)
|
|||
else pb = &Neighbor::half_bin_no_newton_ghost_omp;
|
||||
} else if (triclinic == 0) {
|
||||
pb = &Neighbor::half_bin_newton_omp;
|
||||
} else if (triclinic == 1)
|
||||
} else if (triclinic == 1)
|
||||
pb = &Neighbor::half_bin_newton_tri_omp;
|
||||
} else if (rq->newton == 1) {
|
||||
if (triclinic == 0) pb = &Neighbor::half_bin_newton_omp;
|
||||
|
|
|
@ -472,7 +472,7 @@ void Output::reset_timestep(bigint ntimestep)
|
|||
if (restart_every_single) {
|
||||
next_restart_single =
|
||||
(ntimestep/restart_every_single)*restart_every_single;
|
||||
if (next_restart_single < ntimestep)
|
||||
if (next_restart_single < ntimestep)
|
||||
next_restart_single += restart_every_single;
|
||||
} else {
|
||||
modify->clearstep_compute();
|
||||
|
@ -491,7 +491,7 @@ void Output::reset_timestep(bigint ntimestep)
|
|||
if (restart_every_double) {
|
||||
next_restart_double =
|
||||
(ntimestep/restart_every_double)*restart_every_double;
|
||||
if (next_restart_double < ntimestep)
|
||||
if (next_restart_double < ntimestep)
|
||||
next_restart_double += restart_every_double;
|
||||
} else {
|
||||
modify->clearstep_compute();
|
||||
|
@ -507,7 +507,7 @@ void Output::reset_timestep(bigint ntimestep)
|
|||
} else next_restart_double = update->laststep + 1;
|
||||
|
||||
next_restart = MIN(next_restart_single,next_restart_double);
|
||||
|
||||
|
||||
if (var_thermo) {
|
||||
modify->clearstep_compute();
|
||||
update->ntimestep--;
|
||||
|
@ -522,7 +522,7 @@ void Output::reset_timestep(bigint ntimestep)
|
|||
next_thermo = (ntimestep/thermo_every)*thermo_every;
|
||||
if (next_thermo < ntimestep) next_thermo += thermo_every;
|
||||
next_thermo = MIN(next_thermo,update->laststep);
|
||||
} else next_thermo = update->laststep;
|
||||
} else next_thermo = update->laststep;
|
||||
|
||||
next = MIN(next_dump_any,next_restart);
|
||||
next = MIN(next,next_thermo);
|
||||
|
|
|
@ -57,7 +57,7 @@ class Pair : protected Pointers {
|
|||
int evflag; // energy,virial settings
|
||||
int eflag_either,eflag_global,eflag_atom;
|
||||
int vflag_either,vflag_global,vflag_atom;
|
||||
|
||||
|
||||
int ncoultablebits; // size of Coulomb table, accessed by KSpace
|
||||
|
||||
int nextra; // # of extra quantities pair style calculates
|
||||
|
|
|
@ -1,443 +1,442 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_lj_cut_coul_cut.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulCut::~PairLJCutCoulCut()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(cut_coul);
|
||||
memory->destroy(cut_coulsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
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;
|
||||
|
||||
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;
|
||||
}
|
||||
|
||||
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(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
|
||||
memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_lj_global = force->numeric(arg[0]);
|
||||
if (narg == 1) cut_coul_global = cut_lj_global;
|
||||
else cut_coul_global = force->numeric(arg[1]);
|
||||
|
||||
// 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_lj[i][j] = cut_lj_global;
|
||||
cut_coul[i][j] = cut_coul_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(arg[2]);
|
||||
double sigma_one = force->numeric(arg[3]);
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
double cut_coul_one = cut_coul_global;
|
||||
if (narg >= 5) cut_coul_one = cut_lj_one = force->numeric(arg[4]);
|
||||
if (narg == 6) cut_coul_one = force->numeric(arg[5]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
cut_coul[i][j] = cut_coul_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style lj/cut/coul/cut requires atom attribute q");
|
||||
|
||||
neighbor->request(this);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulCut::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][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]);
|
||||
}
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][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_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];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double sig2 = sigma[i][j]*sigma[i][j];
|
||||
double sig6 = sig2*sig2*sig2;
|
||||
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
|
||||
double rc6 = rc3*rc3;
|
||||
double rc9 = rc3*rc6;
|
||||
etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
|
||||
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
|
||||
ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
|
||||
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
|
||||
}
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulCut::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
forcecoul = force->qqrd2e * atom->q[i]*atom->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;
|
||||
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
|
||||
eng += factor_coul*phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
eng += factor_lj*philj;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJCutCoulCut::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
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
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_lj_cut_coul_cut.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairLJCutCoulCut::~PairLJCutCoulCut()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(cut_coul);
|
||||
memory->destroy(cut_coulsq);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
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;
|
||||
|
||||
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;
|
||||
}
|
||||
|
||||
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(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
|
||||
memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_lj_global = force->numeric(arg[0]);
|
||||
if (narg == 1) cut_coul_global = cut_lj_global;
|
||||
else cut_coul_global = force->numeric(arg[1]);
|
||||
|
||||
// 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_lj[i][j] = cut_lj_global;
|
||||
cut_coul[i][j] = cut_coul_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(arg[2]);
|
||||
double sigma_one = force->numeric(arg[3]);
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
double cut_coul_one = cut_coul_global;
|
||||
if (narg >= 5) cut_coul_one = cut_lj_one = force->numeric(arg[4]);
|
||||
if (narg == 6) cut_coul_one = force->numeric(arg[5]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
cut_coul[i][j] = cut_coul_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style lj/cut/coul/cut requires atom attribute q");
|
||||
|
||||
neighbor->request(this);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulCut::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][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]);
|
||||
}
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][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_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];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double sig2 = sigma[i][j]*sigma[i][j];
|
||||
double sig6 = sig2*sig2*sig2;
|
||||
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
|
||||
double rc6 = rc3*rc3;
|
||||
double rc9 = rc3*rc6;
|
||||
etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
|
||||
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
|
||||
ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
|
||||
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
|
||||
}
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
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);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLJCutCoulCut::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairLJCutCoulCut::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
forcecoul = force->qqrd2e * atom->q[i]*atom->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;
|
||||
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
|
||||
eng += factor_coul*phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
eng += factor_lj*philj;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairLJCutCoulCut::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
return NULL;
|
||||
}
|
||||
|
|
|
@ -1,74 +1,74 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/cut,PairLJCutCoulCut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_CUT_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulCut : public Pair {
|
||||
public:
|
||||
PairLJCutCoulCut(class LAMMPS *);
|
||||
virtual ~PairLJCutCoulCut();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global,cut_coul_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double **cut_coul,**cut_coulsq;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style lj/cut/coul/cut requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
*/
|
||||
/* ----------------------------------------------------------------------
|
||||
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
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(lj/cut/coul/cut,PairLJCutCoulCut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_CUT_COUL_CUT_H
|
||||
#define LMP_PAIR_LJ_CUT_COUL_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLJCutCoulCut : public Pair {
|
||||
public:
|
||||
PairLJCutCoulCut(class LAMMPS *);
|
||||
virtual ~PairLJCutCoulCut();
|
||||
virtual void compute(int, int);
|
||||
virtual void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
virtual void write_restart_settings(FILE *);
|
||||
virtual void read_restart_settings(FILE *);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global,cut_coul_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double **cut_coul,**cut_coulsq;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style lj/cut/coul/cut requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
*/
|
||||
|
|
|
@ -729,7 +729,7 @@ void ReadDump::process_atoms(int n)
|
|||
|
||||
// replace image flag in case changed by ix,iy,iz fields
|
||||
|
||||
image[m] = ((tagint) xbox << IMG2BITS) |
|
||||
image[m] = ((tagint) xbox << IMG2BITS) |
|
||||
((tagint) ybox << IMGBITS) | zbox;
|
||||
}
|
||||
}
|
||||
|
@ -814,7 +814,7 @@ void ReadDump::process_atoms(int n)
|
|||
|
||||
// replace image flag in case changed by ix,iy,iz fields
|
||||
|
||||
image[m] = ((tagint) xbox << IMG2BITS) |
|
||||
image[m] = ((tagint) xbox << IMG2BITS) |
|
||||
((tagint) ybox << IMGBITS) | zbox;
|
||||
}
|
||||
}
|
||||
|
@ -881,4 +881,3 @@ double ReadDump::zfield(int i, int j)
|
|||
if (scaled == UNSCALED) return fields[i][j];
|
||||
return fields[i][j]*zprd + zlo;
|
||||
}
|
||||
|
||||
|
|
|
@ -127,7 +127,7 @@ bigint ReaderXYZ::read_header(double box[3][3], int &triclinic,
|
|||
|
||||
memory->create(fieldindex,nfield,"read_dump:fieldindex");
|
||||
|
||||
// for xyz we know nothing about the style of coordinates,
|
||||
// for xyz we know nothing about the style of coordinates,
|
||||
// so the caller has to set the proper flag.
|
||||
|
||||
xflag = scaledflag;
|
||||
|
@ -148,7 +148,7 @@ bigint ReaderXYZ::read_header(double box[3][3], int &triclinic,
|
|||
fieldflag = 1;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return natoms;
|
||||
}
|
||||
|
||||
|
|
|
@ -278,7 +278,7 @@ void Replicate::command(int narg, char **arg)
|
|||
|
||||
m = 0;
|
||||
while (m < n) {
|
||||
image = ((tagint) IMGMAX << IMG2BITS) |
|
||||
image = ((tagint) IMGMAX << IMG2BITS) |
|
||||
((tagint) IMGMAX << IMGBITS) | IMGMAX;
|
||||
if (triclinic == 0) {
|
||||
x[0] = buf[m+1] + ix*old_xprd;
|
||||
|
|
|
@ -108,7 +108,7 @@ void Rerun::command(int narg, char **arg)
|
|||
int nremain = narg - iarg - 1;
|
||||
if (nremain <= 0) error->all(FLERR,"Illegal rerun command");
|
||||
if (first > last) error->all(FLERR,"Illegal rerun command");
|
||||
if (startflag && stopflag && start > stop)
|
||||
if (startflag && stopflag && start > stop)
|
||||
error->all(FLERR,"Illegal rerun command");
|
||||
|
||||
// pass list of filenames to ReadDump
|
||||
|
@ -117,7 +117,7 @@ void Rerun::command(int narg, char **arg)
|
|||
ReadDump *rd = new ReadDump(lmp);
|
||||
|
||||
rd->store_files(nfile,arg);
|
||||
if (nremain)
|
||||
if (nremain)
|
||||
nremain = rd->fields_and_keywords(nremain,&arg[narg-nremain]);
|
||||
else nremain = rd->fields_and_keywords(0,NULL);
|
||||
if (nremain) rd->setup_reader(nremain,&arg[narg-nremain]);
|
||||
|
|
|
@ -497,7 +497,7 @@ void Set::set(int keyword)
|
|||
if (yimageflag) ybox = yimage;
|
||||
if (zimageflag) zbox = zimage;
|
||||
atom->image[i] = ((zbox + (tagint) IMGMAX & IMGMASK) << IMG2BITS) |
|
||||
((ybox + (tagint) IMGMAX & IMGMASK) << IMGBITS) |
|
||||
((ybox + (tagint) IMGMAX & IMGMASK) << IMGBITS) |
|
||||
(xbox + IMGMAX & IMGMASK);
|
||||
|
||||
// set dipole moment
|
||||
|
|
|
@ -164,7 +164,7 @@ void Variable::set(int narg, char **arg)
|
|||
} else if (narg == 4 || (narg == 5 && strcmp(arg[4],"pad") == 0)) {
|
||||
nfirst = atoi(arg[2]);
|
||||
nlast = atoi(arg[3]);
|
||||
if (nfirst > nlast || nlast < 0)
|
||||
if (nfirst > nlast || nlast < 0)
|
||||
error->all(FLERR,"Illegal variable command");
|
||||
if (narg == 5 && strcmp(arg[4],"pad") == 0) {
|
||||
char digits[12];
|
||||
|
@ -924,7 +924,7 @@ double Variable::evaluate(char *str, Tree **tree)
|
|||
newtree->type = ATOMARRAY;
|
||||
if (compute->array_atom)
|
||||
newtree->array = &compute->array_atom[0][index1-1];
|
||||
else
|
||||
else
|
||||
newtree->array = NULL;
|
||||
newtree->nstride = compute->size_peratom_cols;
|
||||
newtree->left = newtree->middle = newtree->right = NULL;
|
||||
|
@ -1093,7 +1093,7 @@ double Variable::evaluate(char *str, Tree **tree)
|
|||
newtree->type = ATOMARRAY;
|
||||
if (fix->array_atom)
|
||||
newtree->array = &fix->array_atom[0][index1-1];
|
||||
else
|
||||
else
|
||||
newtree->array = NULL;
|
||||
newtree->nstride = fix->size_peratom_cols;
|
||||
newtree->left = newtree->middle = newtree->right = NULL;
|
||||
|
|
Loading…
Reference in New Issue