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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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97
src/fix_ave_spatial.cpp
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@ -43,15 +43,12 @@ enum{ONE,RUNNING,WINDOW};
#define INVOKED_PERATOM 8
#define BIG 1000000000
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix ave/spatial command");
if (narg < 6) error->all(FLERR,"Illegal fix ave/spatial command");
MPI_Comm_rank(world,&me);
@ -73,7 +70,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
else break;
if (dim[ndim] == 2 && domain->dimension == 2)
error->all("Cannot use fix ave/spatial z for 2 dimensional model");
error->all(FLERR,"Cannot use fix ave/spatial z for 2 dimensional model");
if (strcmp(arg[iarg+1],"lower") == 0) originflag[ndim] = LOWER;
if (strcmp(arg[iarg+1],"center") == 0) originflag[ndim] = CENTER;
@ -86,11 +83,11 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
iarg += 3;
}
if (!ndim) error->all("Illegal fix ave/spatial command");
if (!ndim) error->all(FLERR,"Illegal fix ave/spatial command");
if (ndim == 2 && dim[0] == dim[1])
error->all("Same dimension twice in fix ave/spatial");
error->all(FLERR,"Same dimension twice in fix ave/spatial");
if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
error->all("Same dimension twice in fix ave/spatial");
error->all(FLERR,"Same dimension twice in fix ave/spatial");
// parse values until one isn't recognized
@ -144,7 +141,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/spatial command");
error->all(FLERR,"Illegal fix ave/spatial command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
@ -175,125 +172,125 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"all") == 0) normflag = ALL;
else if (strcmp(arg[iarg+1],"sample") == 0) normflag = SAMPLE;
else error->all("Illegal fix ave/spatial command");
else error->all(FLERR,"Illegal fix ave/spatial command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
else if (strcmp(arg[iarg+1],"reduced") == 0) scaleflag = REDUCED;
else error->all("Illegal fix ave/spatial command");
else error->all(FLERR,"Illegal fix ave/spatial command");
iarg += 2;
} else if (strcmp(arg[iarg],"region") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
iregion = domain->find_region(arg[iarg+1]);
if (iregion == -1)
error->all("Region ID for fix ave/spatial does not exist");
error->all(FLERR,"Region ID for fix ave/spatial does not exist");
int n = strlen(arg[iarg+1]) + 1;
idregion = new char[n];
strcpy(idregion,arg[iarg+1]);
regionflag = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
error->one(str);
error->one(FLERR,str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all("Illegal fix ave/spatial command");
else error->all(FLERR,"Illegal fix ave/spatial command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
nwindow = atoi(arg[iarg+2]);
if (nwindow <= 0) error->all("Illegal fix ave/spatial command");
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all("Illegal fix ave/spatial command");
} else error->all(FLERR,"Illegal fix ave/spatial command");
}
// setup and error check
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all("Illegal fix ave/spatial command");
error->all(FLERR,"Illegal fix ave/spatial command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/spatial command");
if (delta[0] <= 0.0) error->all("Illegal fix ave/spatial command");
error->all(FLERR,"Illegal fix ave/spatial command");
if (delta[0] <= 0.0) error->all(FLERR,"Illegal fix ave/spatial command");
if (ndim >= 2 && delta[1] <= 0.0)
error->all("Illegal fix ave/spatial command");
error->all(FLERR,"Illegal fix ave/spatial command");
if (ndim == 3 && delta[2] <= 0.0)
error->all("Illegal fix ave/spatial command");
error->all(FLERR,"Illegal fix ave/spatial command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/spatial compute does not "
error->all(FLERR,"Fix ave/spatial compute does not "
"calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all("Fix ave/spatial compute does not "
error->all(FLERR,"Fix ave/spatial compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all("Fix ave/spatial compute does not "
error->all(FLERR,"Fix ave/spatial compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all("Fix ave/spatial compute vector is accessed out-of-range");
error->all(FLERR,"Fix ave/spatial compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/spatial fix does not calculate per-atom values");
error->all(FLERR,"Fix ave/spatial fix does not calculate per-atom values");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols != 0)
error->all("Fix ave/spatial fix does not calculate a per-atom vector");
error->all(FLERR,"Fix ave/spatial fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all("Fix ave/spatial fix does not calculate a per-atom array");
error->all(FLERR,"Fix ave/spatial fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all("Fix ave/spatial fix vector is accessed out-of-range");
error->all(FLERR,"Fix ave/spatial fix vector is accessed out-of-range");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all("Variable name for fix ave/spatial does not exist");
error->all(FLERR,"Variable name for fix ave/spatial does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/spatial variable is not atom-style variable");
error->all(FLERR,"Fix ave/spatial variable is not atom-style variable");
}
}
@ -330,10 +327,10 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
int triclinic = domain->triclinic;
if (triclinic == 1 && scaleflag != REDUCED)
error->all("Fix ave/spatial for triclinic boxes requires units reduced");
error->all(FLERR,"Fix ave/spatial for triclinic boxes requires units reduced");
if (scaleflag == LATTICE && domain->lattice == NULL)
error->all("Use of fix ave/spatial with undefined lattice");
error->all(FLERR,"Use of fix ave/spatial with undefined lattice");
if (scaleflag == LATTICE) {
xscale = domain->lattice->xlattice;
@ -429,7 +426,7 @@ void FixAveSpatial::init()
if (regionflag) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all("Region ID for fix ave/spatial does not exist");
error->all(FLERR,"Region ID for fix ave/spatial does not exist");
region = domain->regions[iregion];
}
@ -437,7 +434,7 @@ void FixAveSpatial::init()
if (ave == RUNNING || ave == WINDOW) {
if (scaleflag != REDUCED && domain->box_change)
error->all("Fix ave/spatial settings invalid with changing box");
error->all(FLERR,"Fix ave/spatial settings invalid with changing box");
}
// set indices and check validity of all computes,fixes,variables
@ -447,22 +444,22 @@ void FixAveSpatial::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all("Fix ID for fix ave/spatial does not exist");
error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
value2index[m] = ifix;
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Fix for fix ave/spatial not computed at compatible time");
error->all(FLERR,"Fix for fix ave/spatial not computed at compatible time");
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all("Variable name for fix ave/spatial does not exist");
error->all(FLERR,"Variable name for fix ave/spatial does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;