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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3951 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-04-02 16:53:40 +00:00
parent 02ac8178c5
commit 75c51a178d
30 changed files with 3477 additions and 3896 deletions
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216
src/fix_press_berendsen.cpp
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@ -33,7 +33,8 @@ using namespace LAMMPS_NS;
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
enum{NOBIAS,BIAS};
enum{XYZ,XY,YZ,XZ,ANISO};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO};
/* ---------------------------------------------------------------------- */
@ -44,80 +45,89 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
box_change = 1;
// Berendsen barostat should be applied every step
// Berendsen barostat applied every step
nevery = 1;
if (strcmp(arg[3],"xyz") == 0) {
if (narg < 7) error->all("Illegal fix press/berendsen command");
press_couple = XYZ;
p_start[0] = p_start[1] = p_start[2] = atof(arg[4]);
p_stop[0] = p_stop[1] = p_stop[2] = atof(arg[5]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[6]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
} else {
if (strcmp(arg[3],"xy") == 0) press_couple = XY;
else if (strcmp(arg[3],"yz") == 0) press_couple = YZ;
else if (strcmp(arg[3],"xz") == 0) press_couple = XZ;
else if (strcmp(arg[3],"aniso") == 0) press_couple = ANISO;
else error->all("Illegal fix press/berendsen command");
if (narg < 8) error->all("Illegal fix press/berendsen command");
if (domain->dimension == 2 &&
(press_couple == XY || press_couple == YZ || press_couple == XZ))
error->all("Invalid fix press/berendsen command for a 2d simulation");
if (strcmp(arg[4],"NULL") == 0) {
p_start[0] = p_stop[0] = p_period[0] = 0.0;
p_flag[0] = 0;
} else {
p_start[0] = atof(arg[4]);
p_stop[0] = atof(arg[5]);
p_flag[0] = 1;
}
if (strcmp(arg[6],"NULL") == 0) {
p_start[1] = p_stop[1] = p_period[1] = 0.0;
p_flag[1] = 0;
} else {
p_start[1] = atof(arg[6]);
p_stop[1] = atof(arg[7]);
p_flag[1] = 1;
}
if (strcmp(arg[8],"NULL") == 0) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
} else {
if (domain->dimension == 2)
error->all("Invalid fix press/berendsen command for a 2d simulation");
p_start[2] = atof(arg[8]);
p_stop[2] = atof(arg[9]);
p_flag[2] = 1;
}
double period = atof(arg[10]);
if (p_flag[0]) p_period[0] = period;
if (p_flag[1]) p_period[1] = period;
if (p_flag[2]) p_period[2] = period;
}
// process extra keywords
// default values
pcouple = NONE;
bulkmodulus = 10.0;
allremap = 1;
int iarg;
if (press_couple == XYZ) iarg = 7;
else iarg = 11;
for (int i = 0; i < 3; i++) {
p_start[i] = p_stop[i] = p_period[i] = 0.0;
p_flag[i] = 0;
p_period[i] = 0.0;
}
// process keywords
dimension = domain->dimension;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"modulus") == 0) {
if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all("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]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all("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]);
p_period[0] = p_period[1] = p_period[2] = atof(arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all("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");
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");
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 command for a 2d simulation");
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all("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");
iarg += 2;
} else if (strcmp(arg[iarg],"modulus") == 0) {
if (iarg+2 > narg) error->all("Illegal fix press/berendsen command");
bulkmodulus = atof(arg[iarg+1]);
if (bulkmodulus <= 0.0)
@ -134,21 +144,18 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
// error checks
if (press_couple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (press_couple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (press_couple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (dimension == 2 && p_flag[2])
error->all("Invalid fix press/berendsen command for a 2d simulation");
if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
error->all("Invalid fix press/berendsen command for a 2d simulation");
if (press_couple == XY &&
(p_start[0] != p_start[1] || p_stop[0] != p_stop[1]))
if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (press_couple == YZ &&
(p_start[1] != p_start[2] || p_stop[1] != p_stop[2]))
if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (press_couple == XZ &&
(p_start[0] != p_start[2] || p_stop[0] != p_stop[2]))
if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
error->all("Invalid fix press/berendsen command pressure settings");
if (p_flag[0] && domain->xperiodic == 0)
@ -158,12 +165,34 @@ FixPressBerendsen::FixPressBerendsen(LAMMPS *lmp, int narg, char **arg) :
if (p_flag[2] && domain->zperiodic == 0)
error->all("Cannot use fix press/berendsen on a non-periodic dimension");
if (p_flag[0] && p_period[0] <= 0.0)
error->all("Fix press/berendsen period must be > 0.0");
if (p_flag[1] && p_period[1] <= 0.0)
error->all("Fix press/berendsen period must be > 0.0");
if (p_flag[2] && p_period[2] <= 0.0)
error->all("Fix press/berendsen period must be > 0.0");
if (pcouple == XYZ &&
(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");
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");
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");
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");
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");
// pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
// else pstyle = ANISO -> 3 dof
if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO;
else pstyle = ANISO;
// create a new compute temp style
// id = fix-ID + temp
@ -235,13 +264,15 @@ void FixPressBerendsen::init()
if (domain->triclinic)
error->all("Cannot use fix press/berendsen with triclinic box");
// insure no conflict with fix deform
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"deform") == 0) {
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 "
"fix deform on same dimension");
"fix deform on same component of stress tensor");
}
// set temperature and pressure ptrs
@ -298,7 +329,7 @@ void FixPressBerendsen::end_of_step()
{
// compute new T,P
if (press_couple == XYZ) {
if (pstyle == ISO) {
double tmp = temperature->compute_scalar();
tmp = pressure->compute_scalar();
} else {
@ -336,21 +367,24 @@ void FixPressBerendsen::couple()
{
double *tensor = pressure->vector;
if (press_couple == XYZ)
if (pstyle == ISO)
p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
else if (press_couple == XY) {
else if (pcouple == XYZ) {
double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
p_current[0] = p_current[1] = p_current[2] = ave;
} else if (pcouple == XY) {
double ave = 0.5 * (tensor[0] + tensor[1]);
p_current[0] = p_current[1] = ave;
p_current[2] = tensor[2];
} else if (press_couple == YZ) {
} else if (pcouple == YZ) {
double ave = 0.5 * (tensor[1] + tensor[2]);
p_current[1] = p_current[2] = ave;
p_current[0] = tensor[0];
} else if (press_couple == XZ) {
} else if (pcouple == XZ) {
double ave = 0.5 * (tensor[0] + tensor[2]);
p_current[0] = p_current[2] = ave;
p_current[1] = tensor[1];
} if (press_couple == ANISO) {
} else {
p_current[0] = tensor[0];
p_current[1] = tensor[1];
p_current[2] = tensor[2];