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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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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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87
src/fix_press_berendsen.cpp
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@ -29,9 +29,6 @@
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};
@ -41,7 +38,7 @@ enum{ISO,ANISO};
FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all("Illegal fix press/berendsen command");
if (narg < 5) error->all(FLERR,"Illegal fix press/berendsen command");
box_change = 1;
box_change_size = 1;
@ -70,7 +67,7 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix press/berendsen 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]);
@ -82,7 +79,7 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix press/berendsen 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]);
@ -95,52 +92,52 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix press/berendsen command");
p_start[0] = atof(arg[iarg+1]);
p_stop[0] = atof(arg[iarg+2]);
p_period[0] = atof(arg[iarg+3]);
p_flag[0] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix press/berendsen command");
p_start[1] = atof(arg[iarg+1]);
p_stop[1] = atof(arg[iarg+2]);
p_period[1] = atof(arg[iarg+3]);
p_flag[1] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+4 > narg) error->all(FLERR,"Illegal fix press/berendsen command");
p_start[2] = atof(arg[iarg+1]);
p_stop[2] = atof(arg[iarg+2]);
p_period[2] = atof(arg[iarg+3]);
p_flag[2] = 1;
iarg += 4;
if (dimension == 2)
error->all("Invalid fix press/berendsen for a 2d simulation");
error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix press/berendsen 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 press/berendsen command");
else error->all(FLERR,"Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg],"modulus") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix press/berendsen command");
bulkmodulus = atof(arg[iarg+1]);
if (bulkmodulus <= 0.0)
error->all("Illegal fix press/berendsen command");
error->all(FLERR,"Illegal fix press/berendsen command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix press/berendsen 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 press/berendsen command");
else error->all(FLERR,"Illegal fix press/berendsen command");
iarg += 2;
} else error->all("Illegal fix press/berendsen command");
} else error->all(FLERR,"Illegal fix press/berendsen command");
}
if (allremap == 0) restart_pbc = 1;
@ -148,54 +145,54 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
// error checks
if (dimension == 2 && p_flag[2])
error->all("Invalid fix press/berendsen for a 2d simulation");
error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all("Invalid fix press/berendsen for a 2d simulation");
error->all(FLERR,"Invalid fix press/berendsen for a 2d simulation");
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
error->all("Invalid fix press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
error->all(FLERR,"Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[1] && domain->yperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
error->all(FLERR,"Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[2] && domain->zperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
error->all(FLERR,"Cannot use fix press/berendsen on a non-periodic dimension");
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 press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen 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 press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen 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 press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen 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 press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen 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 press/berendsen pressure settings");
error->all(FLERR,"Invalid fix press/berendsen pressure settings");
if ((p_flag[0] && p_period[0] <= 0.0) ||
(p_flag[1] && p_period[1] <= 0.0) ||
(p_flag[2] && p_period[2] <= 0.0))
error->all("Fix press/berendsen damping parameters must be > 0.0");
error->all(FLERR,"Fix press/berendsen damping parameters must be > 0.0");
// pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
// else pstyle = ANISO -> 3 dof
@ -271,7 +268,7 @@ int FixPressBerendsen::setmask()
void FixPressBerendsen::init()
{
if (domain->triclinic)
error->all("Cannot use fix press/berendsen with triclinic box");
error->all(FLERR,"Cannot use fix press/berendsen with triclinic box");
// insure no conflict with fix deform
@ -280,7 +277,7 @@ void FixPressBerendsen::init()
int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]))
error->all("Cannot use fix press/berendsen and "
error->all(FLERR,"Cannot use fix press/berendsen and "
"fix deform on same component of stress tensor");
}
@ -288,7 +285,7 @@ void FixPressBerendsen::init()
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all("Temperature ID for fix press/berendsen does not exist");
error->all(FLERR,"Temperature ID for fix press/berendsen does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
@ -296,7 +293,7 @@ void FixPressBerendsen::init()
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all("Pressure ID for fix press/berendsen does not exist");
error->all(FLERR,"Pressure ID for fix press/berendsen does not exist");
pressure = modify->compute[icompute];
// Kspace setting
@ -462,7 +459,7 @@ void FixPressBerendsen::remap()
int FixPressBerendsen::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;
@ -473,25 +470,25 @@ int FixPressBerendsen::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 NPT is not for group all");
error->warning(FLERR,"Temperature for NPT is not for group all");
// reset id_temp of pressure to new temperature ID
icompute = modify->find_compute(id_press);
if (icompute < 0)
error->all("Pressure ID for fix press/berendsen does not exist");
error->all(FLERR,"Pressure ID for fix press/berendsen 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 (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (pflag) {
modify->delete_compute(id_press);
pflag = 0;
@ -502,11 +499,11 @@ int FixPressBerendsen::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;
}
return 0;