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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7003 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-09-23 18:06:55 +00:00
parent 2d99de131d
commit 19e8c92a90
468 changed files with 4628 additions and 5204 deletions
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139
src/USER-CUDA/fix_nh_cuda.cpp
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@ -38,9 +38,6 @@
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
enum{NOBIAS,BIAS};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
@ -53,9 +50,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
cuda = lmp->cuda;
if(cuda == NULL)
error->all("You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
error->all(FLERR,"You cannot use a /cuda class, without activating 'cuda' acceleration. Provide '-c on' as command-line argument to LAMMPS..");
if (narg < 4) error->all("Illegal fix nvt/npt/nph command");
if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command");
restart_global = 1;
time_integrate = 1;
@ -98,17 +95,17 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
while (iarg < narg) {
if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
tstat_flag = 1;
t_start = atof(arg[iarg+1]);
t_stop = atof(arg[iarg+2]);
t_period = atof(arg[iarg+3]);
if (t_start < 0.0 || t_stop <= 0.0)
error->all("Target T for fix nvt/npt/nph cannot be 0.0");
error->all(FLERR,"Target T for fix nvt/npt/nph cannot be 0.0");
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
@ -120,7 +117,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
@ -132,7 +129,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
}
iarg += 4;
} else if (strcmp(arg[iarg],"tri") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
pcouple = NONE;
p_start[0] = p_start[1] = p_start[2] = atof(arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[iarg+2]);
@ -153,7 +150,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[0] = atof(arg[iarg+1]);
p_stop[0] = atof(arg[iarg+2]);
p_period[0] = atof(arg[iarg+3]);
@ -161,7 +158,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[1] = atof(arg[iarg+1]);
p_stop[1] = atof(arg[iarg+2]);
p_period[1] = atof(arg[iarg+3]);
@ -169,7 +166,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
deviatoric_flag = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[2] = atof(arg[iarg+1]);
p_stop[2] = atof(arg[iarg+2]);
p_period[2] = atof(arg[iarg+3]);
@ -177,10 +174,10 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix nvt/npt/nph command for a 2d simulation");
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"yz") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[3] = atof(arg[iarg+1]);
p_stop[3] = atof(arg[iarg+2]);
p_period[3] = atof(arg[iarg+3]);
@ -188,9 +185,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix nvt/npt/nph command for a 2d simulation");
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xz") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[4] = atof(arg[iarg+1]);
p_stop[4] = atof(arg[iarg+2]);
p_period[4] = atof(arg[iarg+3]);
@ -198,9 +195,9 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
deviatoric_flag = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix nvt/npt/nph command for a 2d simulation");
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
} else if (strcmp(arg[iarg],"xy") == 0) {
if (iarg+4 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
p_start[5] = atof(arg[iarg+1]);
p_stop[5] = atof(arg[iarg+2]);
p_period[5] = atof(arg[iarg+3]);
@ -209,116 +206,116 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ;
else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE;
else error->all("Illegal fix nvt/npt/nph command");
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"drag") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
drag = atof(arg[iarg+1]);
if (drag < 0.0) error->all("Illegal fix nvt/npt/nph command");
if (drag < 0.0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else if (strcmp(arg[iarg+1],"partial") == 0) allremap = 0;
else error->all("Illegal fix nvt/npt/nph command");
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"tchain") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
mtchain = atoi(arg[iarg+1]);
if (mtchain < 1) error->all("Illegal fix nvt/npt/nph command");
if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
mpchain = atoi(arg[iarg+1]);
if (mpchain < 0) error->all("Illegal fix nvt/npt/nph command");
if (mpchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"mtk") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
else error->all("Illegal fix nvt/npt/nph command");
else error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"tloop") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
nc_tchain = atoi(arg[iarg+1]);
if (nc_tchain < 0) error->all("Illegal fix nvt/npt/nph command");
if (nc_tchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"ploop") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
nc_pchain = atoi(arg[iarg+1]);
if (nc_pchain < 0) error->all("Illegal fix nvt/npt/nph command");
if (nc_pchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else if (strcmp(arg[iarg],"nreset") == 0) {
if (iarg+2 > narg) error->all("Illegal fix nvt/npt/nph command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
nreset_h0 = atoi(arg[iarg+1]);
if (nreset_h0 < 0) error->all("Illegal fix nvt/npt/nph command");
if (nreset_h0 < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
iarg += 2;
} else error->all("Illegal fix nvt/npt/nph command");
} else error->all(FLERR,"Illegal fix nvt/npt/nph command");
}
// error checks
if (dimension == 2 && (p_flag[2] || p_flag[3] || p_flag[4]))
error->all("Invalid fix nvt/npt/nph command for a 2d simulation");
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all("Invalid fix nvt/npt/nph command for a 2d simulation");
error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix nvt/npt/nph command pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all("Invalid fix nvt/npt/nph command pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix nvt/npt/nph command pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix nvt/npt/nph command pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix nvt/npt/nph command pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix nvt/npt/nph on a non-periodic dimension");
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all("Cannot use fix nvt/npt/nph on a non-periodic dimension");
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all("Cannot use fix nvt/npt/nph on a non-periodic dimension");
error->all(FLERR,"Cannot use fix nvt/npt/nph on a non-periodic dimension");
if (p_flag[3] && domain->zperiodic == 0)
error->all("Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[4] && domain->zperiodic == 0)
error->all("Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (p_flag[5] && domain->yperiodic == 0)
error->all("Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
error->all(FLERR,"Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
error->all("Can not specify Pxy/Pxz/Pyz in "
error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
"fix nvt/npt/nph with non-triclinic box");
if (pcouple == XYZ && dimension == 3 &&
(p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[1] || p_period[0] != p_period[2]))
error->all("Invalid fix nvt/npt/nph pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XYZ && dimension == 2 &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all("Invalid fix nvt/npt/nph pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XY &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
p_period[0] != p_period[1]))
error->all("Invalid fix nvt/npt/nph pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
p_period[1] != p_period[2]))
error->all("Invalid fix nvt/npt/nph pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if (pcouple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
p_period[0] != p_period[2]))
error->all("Invalid fix nvt/npt/nph pressure settings");
error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
if ((tstat_flag && t_period <= 0.0) ||
(p_flag[0] && p_period[0] <= 0.0) ||
@ -327,7 +324,7 @@ FixNHCuda::FixNHCuda(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
(p_flag[3] && p_period[3] <= 0.0) ||
(p_flag[4] && p_period[4] <= 0.0) ||
(p_flag[5] && p_period[5] <= 0.0))
error->all("Fix nvt/npt/nph damping parameters must be > 0.0");
error->all(FLERR,"Fix nvt/npt/nph damping parameters must be > 0.0");
// set pstat_flag and box change variables
@ -480,7 +477,7 @@ void FixNHCuda::init()
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
error->all("Cannot use fix npt and fix deform on "
error->all(FLERR,"Cannot use fix npt and fix deform on "
"same component of stress tensor");
}
@ -488,7 +485,7 @@ void FixNHCuda::init()
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all("Temperature ID for fix nvt/nph/npt does not exist");
error->all(FLERR,"Temperature ID for fix nvt/nph/npt does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
@ -496,7 +493,7 @@ void FixNHCuda::init()
if (pstat_flag) {
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Pressure ID for fix npt/nph does not exist");
if (icompute < 0) error->all(FLERR,"Pressure ID for fix npt/nph does not exist");
pressure = modify->compute[icompute];
}
@ -1098,7 +1095,7 @@ void FixNHCuda::remap()
if (domain->yz < -0.5*domain->yprd || domain->yz > 0.5*domain->yprd ||
domain->xz < -0.5*domain->xprd || domain->xz > 0.5*domain->xprd ||
domain->xy < -0.5*domain->xprd || domain->xy > 0.5*domain->xprd)
error->all("Fix npt/nph has tilted box too far - "
error->all(FLERR,"Fix npt/nph has tilted box too far - "
"box flips are not yet implemented");
}
@ -1247,7 +1244,7 @@ void FixNHCuda::restart(char *buf)
int FixNHCuda::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all("Illegal fix_modify command");
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (tflag) {
modify->delete_compute(id_temp);
tflag = 0;
@ -1258,28 +1255,28 @@ int FixNHCuda::modify_param(int narg, char **arg)
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all("Could not find fix_modify temperature ID");
if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all("Fix_modify temperature ID does not compute temperature");
error->all(FLERR,"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for fix modify is not for group all");
error->warning(FLERR,"Temperature for fix modify is not for group all");
// reset id_temp of pressure to new temperature ID
if (pstat_flag) {
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all("Pressure ID for fix modify does not exist");
error->all(FLERR,"Pressure ID for fix modify does not exist");
modify->compute[icompute]->reset_extra_compute_fix(id_temp);
}
return 2;
} else if (strcmp(arg[0],"press") == 0) {
if (narg < 2) error->all("Illegal fix_modify command");
if (!pstat_flag) error->all("Illegal fix_modify command");
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command");
if (pflag) {
modify->delete_compute(id_press);
pflag = 0;
@ -1290,11 +1287,11 @@ int FixNHCuda::modify_param(int narg, char **arg)
strcpy(id_press,arg[1]);
int icompute = modify->find_compute(arg[1]);
if (icompute < 0) error->all("Could not find fix_modify pressure ID");
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all("Fix_modify pressure ID does not compute pressure");
error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
return 2;
}