diff --git a/doc/fix.html b/doc/fix.html
index c027dfdbd8..86e63a692d 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -68,7 +68,8 @@ made to the old fix via the fix_modify command.
fix ave/spatial - output per-atom quantities by layer
fix ave/time - output time-averaged compute quantities
fix com - compute a center-of-mass
-fix deposit - add new atoms above a surface
+fix deform - change the simulation box size/shape
+fix deposit - add new atoms above a surface
fix drag - drag atoms towards a defined coordinate
fix efield - impose electric field on system
fix enforce2d - zero out z-dimension velocity and force
@@ -83,10 +84,15 @@ made to the old fix via the fix_modify command.
fix momentum - zero the linear and/or angular momentum of a group of atoms
fix nph - constant NPH time integration via Nose/Hoover
fix npt - constant NPT time integration via Nose/Hoover
+fix npt/asphere - NPT for aspherical particles
fix nve - constant NVE time integration
-fix nve/gran - NVE time integration for granular systems
-fix nve/noforce - NVE integration without forces (v only)
+fix nve/asphere - NVT for aspherical particles
+fix nve/dipole - NVE for point dipolar particles
+fix nve/gran - NVE for granular particles
+fix nve/noforce - NVE without forces (v only)
fix nvt - constant NVT time integration via Nose/Hoover
+fix nvt/asphere - NVT for aspherical particles
+fix nvt/sllod - NVT for NEMD with SLLOD equations
fix orient/fcc - add grain boundary migration force
fix planeforce - constrain atoms to move in a plane
fix poems - constrain clusters of atoms to move as coupled rigid bodies
@@ -104,8 +110,8 @@ made to the old fix via the fix_modify command.
fix tmd - guide a group of atoms to a new configuration
fix viscous - viscous damping for granular simulations
fix wall/gran - frictional wall(s) for granular simulations
-fix wall/lj93 - Lennard-Jones 9-3 wall
fix wall/lj126 - Lennard-Jones 12-6 wall
+fix wall/lj93 - Lennard-Jones 9-3 wall
fix wall/reflect - reflecting wall(s)
fix wiggle - oscillate walls and frozen atoms
diff --git a/doc/fix.txt b/doc/fix.txt
index 9f9144968d..8a6ffe5763 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -65,7 +65,8 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
"fix ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
"fix ave/time"_fix_ave_time.html - output time-averaged compute quantities
"fix com"_fix_com.html - compute a center-of-mass
-"fix deposit"_fix_desosit.html - add new atoms above a surface
+"fix deform"_fix_deform.html - change the simulation box size/shape
+"fix deposit"_fix_deposit.html - add new atoms above a surface
"fix drag"_fix_drag.html - drag atoms towards a defined coordinate
"fix efield"_fix_efield.html - impose electric field on system
"fix enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
@@ -82,11 +83,15 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
of a group of atoms
"fix nph"_fix_nph.html - constant NPH time integration via Nose/Hoover
"fix npt"_fix_npt.html - constant NPT time integration via Nose/Hoover
+"fix npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
"fix nve"_fix_nve.html - constant NVE time integration
-"fix nve/gran"_fix_nve_gran.html - NVE time integration for \
- granular systems
-"fix nve/noforce"_fix_nve_noforce.html - NVE integration without forces (v only)
+"fix nve/asphere"_fix_nve_asphere.html - NVT for aspherical particles
+"fix nve/dipole"_fix_nve_dipole.html - NVE for point dipolar particles
+"fix nve/gran"_fix_nve_gran.html - NVE for granular particles
+"fix nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
"fix nvt"_fix_nvt.html - constant NVT time integration via Nose/Hoover
+"fix nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
+"fix nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
"fix orient/fcc"_fix_orient_fcc.html - add grain boundary migration force
"fix planeforce"_fix_planeforce.html - constrain atoms to move in a plane
"fix poems"_fix_poems.html - constrain clusters of atoms to move \
@@ -110,8 +115,8 @@ Here is an alphabetic list of fix styles defined in LAMMPS:
"fix viscous"_fix_viscous.html - viscous damping for granular simulations
"fix wall/gran"_fix_wall_gran.html - frictional wall(s) for \
granular simulations
-"fix wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall
"fix wall/lj126"_fix_wall_lj126.html - Lennard-Jones 12-6 wall
+"fix wall/lj93"_fix_wall_lj93.html - Lennard-Jones 9-3 wall
"fix wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
"fix wiggle"_fix_wiggle.html - oscillate walls and frozen atoms :ul
diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp
index 65dc36ad10..d22c1cda3e 100755
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@@ -121,7 +121,7 @@ double ComputeTempAsphere::compute_scalar()
double wbody[3];
double rot[3][3];
double t = 0.0;
-
+
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
diff --git a/src/ASPHERE/fix_npt_asphere.cpp b/src/ASPHERE/fix_npt_asphere.cpp
index 147fec0cca..419ad03c32 100755
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
@@ -169,7 +169,6 @@ void FixNPTASphere::final_integrate()
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
-
angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * ang_factor;
angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * ang_factor;
angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * ang_factor;
diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp
index fac56504f1..0d42ae3469 100755
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
@@ -76,7 +76,7 @@ PairGayBerne::~PairGayBerne()
void PairGayBerne::compute(int eflag, int vflag)
{
int i,j,k,m,numneigh,itype,jtype;
- double one_eng,rsq,r2inv,r6inv,forcelj,phi;
+ double one_eng,rsq,r2inv,r6inv,forcelj;
double fforce[3],ttor[3],rtor[3],r12[3];
double a1[3][3],b1[3][3],g1[3][3],a2[3][3],b2[3][3],g2[3][3],temp[3][3];
int *neighs;
@@ -132,17 +132,19 @@ void PairGayBerne::compute(int eflag, int vflag)
if (rsq < cutsq[itype][jtype]) {
switch (form[itype][jtype]) {
- case SPHERE_SPHERE:
+ case SPHERE_SPHERE:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
forcelj *= -r2inv;
- if (eflag) phi = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
+ 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;
default:
@@ -399,7 +401,8 @@ void PairGayBerne::write_restart(FILE *fp)
int i,j;
for (i = 1; i <= atom->ntypes; i++) {
- fwrite(&well[i][0],sizeof(double),3,fp);
+ fwrite(&setwell[i],sizeof(int),1,fp);
+ if (setwell[i]) fwrite(&well[i][0],sizeof(double),3,fp);
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
@@ -418,14 +421,17 @@ void PairGayBerne::write_restart(FILE *fp)
void PairGayBerne::read_restart(FILE *fp)
{
read_restart_settings(fp);
-
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++) {
- if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
- MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
+ if (me == 0) fread(&setwell[i],sizeof(int),1,fp);
+ MPI_Bcast(&setwell[i],1,MPI_INT,0,world);
+ if (setwell[i]) {
+ if (me == 0) fread(&well[i][0],sizeof(double),3,fp);
+ MPI_Bcast(&well[i][0],3,MPI_DOUBLE,0,world);
+ }
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);
diff --git a/src/pair.cpp b/src/pair.cpp
index 0e565dddd4..1bbadd920c 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -122,6 +122,8 @@ void Pair::init()
if (tail_flag && domain->nonperiodic && comm->me == 0)
error->warning("Using pair tail corrections with nonperiodic system");
+ init_style();
+
if (!allocated) error->all("All pair coeffs are not set");
for (i = 1; i <= atom->ntypes; i++)
@@ -144,8 +146,6 @@ void Pair::init()
}
}
}
-
- init_style();
}
/* ----------------------------------------------------------------------