git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -86,7 +86,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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if (!ndim) error->all(FLERR,"Illegal fix ave/spatial command");
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if (ndim == 2 && dim[0] == dim[1])
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error->all(FLERR,"Same dimension twice in fix ave/spatial");
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if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
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if (ndim == 3 && (dim[0] == dim[1] || dim[1] == dim[2] || dim[0] == dim[2]))
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error->all(FLERR,"Same dimension twice in fix ave/spatial");
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// parse values until one isn't recognized
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@ -127,9 +127,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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which[nvalues] = DENSITY_MASS;
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argindex[nvalues++] = 0;
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} else if (strncmp(arg[iarg],"c_",2) == 0 ||
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strncmp(arg[iarg],"f_",2) == 0 ||
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strncmp(arg[iarg],"v_",2) == 0) {
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} else if (strncmp(arg[iarg],"c_",2) == 0 ||
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strncmp(arg[iarg],"f_",2) == 0 ||
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strncmp(arg[iarg],"v_",2) == 0) {
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if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
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else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
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else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
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@ -140,10 +140,10 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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char *ptr = strchr(suffix,'[');
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if (ptr) {
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if (suffix[strlen(suffix)-1] != ']')
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error->all(FLERR,"Illegal fix ave/spatial command");
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argindex[nvalues] = atoi(ptr+1);
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*ptr = '\0';
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if (suffix[strlen(suffix)-1] != ']')
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error->all(FLERR,"Illegal fix ave/spatial command");
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argindex[nvalues] = atoi(ptr+1);
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*ptr = '\0';
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} else argindex[nvalues] = 0;
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n = strlen(suffix) + 1;
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@ -187,8 +187,8 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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} else if (strcmp(arg[iarg],"region") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
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iregion = domain->find_region(arg[iarg+1]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix ave/spatial does not exist");
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix ave/spatial does not exist");
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int n = strlen(arg[iarg+1]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[iarg+1]);
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@ -197,12 +197,12 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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} else if (strcmp(arg[iarg],"file") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
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if (me == 0) {
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fp = fopen(arg[iarg+1],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
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error->one(FLERR,str);
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}
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fp = fopen(arg[iarg+1],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix ave/spatial file %s",arg[iarg+1]);
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error->one(FLERR,str);
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}
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"ave") == 0) {
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@ -212,9 +212,9 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
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else error->all(FLERR,"Illegal fix ave/spatial command");
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if (ave == WINDOW) {
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
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nwindow = atoi(arg[iarg+2]);
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if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial command");
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if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
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nwindow = atoi(arg[iarg+2]);
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if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/spatial command");
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}
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iarg += 2;
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if (ave == WINDOW) iarg++;
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@ -249,52 +249,52 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
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error->all(FLERR,"Illegal fix ave/spatial command");
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if (delta[0] <= 0.0) error->all(FLERR,"Illegal fix ave/spatial command");
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if (ndim >= 2 && delta[1] <= 0.0)
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if (ndim >= 2 && delta[1] <= 0.0)
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error->all(FLERR,"Illegal fix ave/spatial command");
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if (ndim == 3 && delta[2] <= 0.0)
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if (ndim == 3 && delta[2] <= 0.0)
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error->all(FLERR,"Illegal fix ave/spatial command");
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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int icompute = modify->find_compute(ids[i]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
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error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
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if (modify->compute[icompute]->peratom_flag == 0)
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error->all(FLERR,"Fix ave/spatial compute does not "
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"calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all(FLERR,"Fix ave/spatial compute does not "
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"calculate a per-atom vector");
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error->all(FLERR,"Fix ave/spatial compute does not "
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"calculate per-atom values");
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if (argindex[i] == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all(FLERR,"Fix ave/spatial compute does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
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error->all(FLERR,"Fix ave/spatial compute does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->compute[icompute]->size_peratom_cols)
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error->all(FLERR,
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"Fix ave/spatial compute vector is accessed out-of-range");
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error->all(FLERR,"Fix ave/spatial compute does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->compute[icompute]->size_peratom_cols)
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error->all(FLERR,
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"Fix ave/spatial compute vector is accessed out-of-range");
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} else if (which[i] == FIX) {
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int ifix = modify->find_fix(ids[i]);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
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error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
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if (modify->fix[ifix]->peratom_flag == 0)
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error->all(FLERR,
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"Fix ave/spatial fix does not calculate per-atom values");
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error->all(FLERR,
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"Fix ave/spatial fix does not calculate per-atom values");
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols != 0)
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error->all(FLERR,
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"Fix ave/spatial fix does not calculate a per-atom vector");
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error->all(FLERR,
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"Fix ave/spatial fix does not calculate a per-atom vector");
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
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error->all(FLERR,
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"Fix ave/spatial fix does not calculate a per-atom array");
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error->all(FLERR,
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"Fix ave/spatial fix does not calculate a per-atom array");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
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error->all(FLERR,"Fix ave/spatial fix vector is accessed out-of-range");
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error->all(FLERR,"Fix ave/spatial fix vector is accessed out-of-range");
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} else if (which[i] == VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for fix ave/spatial does not exist");
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error->all(FLERR,"Variable name for fix ave/spatial does not exist");
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if (input->variable->atomstyle(ivariable) == 0)
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error->all(FLERR,"Fix ave/spatial variable is not atom-style variable");
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error->all(FLERR,"Fix ave/spatial variable is not atom-style variable");
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}
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}
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@ -303,7 +303,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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if (fp && me == 0) {
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if (title1) fprintf(fp,"%s\n",title1);
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else fprintf(fp,"# Spatial-averaged data for fix %s and group %s\n",
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id,arg[1]);
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id,arg[1]);
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if (title2) fprintf(fp,"%s\n",title2);
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else fprintf(fp,"# Timestep Number-of-bins\n");
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if (title3) fprintf(fp,"%s\n",title3);
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@ -332,7 +332,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
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int triclinic = domain->triclinic;
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if (triclinic == 1 && scaleflag != REDUCED)
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error->all(FLERR,
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"Fix ave/spatial for triclinic boxes requires units reduced");
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"Fix ave/spatial for triclinic boxes requires units reduced");
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if (scaleflag == LATTICE && domain->lattice == NULL)
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error->all(FLERR,"Use of fix ave/spatial with undefined lattice");
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@ -449,23 +449,23 @@ void FixAveSpatial::init()
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if (which[m] == COMPUTE) {
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int icompute = modify->find_compute(ids[m]);
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if (icompute < 0)
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error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
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error->all(FLERR,"Compute ID for fix ave/spatial does not exist");
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value2index[m] = icompute;
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} else if (which[m] == FIX) {
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int ifix = modify->find_fix(ids[m]);
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if (ifix < 0)
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error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
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if (ifix < 0)
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error->all(FLERR,"Fix ID for fix ave/spatial does not exist");
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value2index[m] = ifix;
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if (nevery % modify->fix[ifix]->peratom_freq)
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error->all(FLERR,
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"Fix for fix ave/spatial not computed at compatible time");
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error->all(FLERR,
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"Fix for fix ave/spatial not computed at compatible time");
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} else if (which[m] == VARIABLE) {
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int ivariable = input->variable->find(ids[m]);
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if (ivariable < 0)
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error->all(FLERR,"Variable name for fix ave/spatial does not exist");
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if (ivariable < 0)
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error->all(FLERR,"Variable name for fix ave/spatial does not exist");
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value2index[m] = ivariable;
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} else value2index[m] = -1;
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@ -553,15 +553,15 @@ void FixAveSpatial::end_of_step()
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double **attribute;
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if (which[m] == V) attribute = atom->v;
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else attribute = atom->f;
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if (regionflag == 0) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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values_one[bin[i]][m] += attribute[i][j];
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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values_one[bin[i]][m] += attribute[i][j];
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
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values_one[bin[i]][m] += attribute[i][j];
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
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values_one[bin[i]][m] += attribute[i][j];
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}
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// DENSITY_NUMBER adds 1 to values
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@ -569,13 +569,13 @@ void FixAveSpatial::end_of_step()
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} else if (which[m] == DENSITY_NUMBER) {
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if (regionflag == 0) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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values_one[bin[i]][m] += 1.0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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values_one[bin[i]][m] += 1.0;
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
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values_one[bin[i]][m] += 1.0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
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values_one[bin[i]][m] += 1.0;
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}
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// DENSITY_MASS adds mass to values
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@ -586,17 +586,17 @@ void FixAveSpatial::end_of_step()
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double *rmass = atom->rmass;
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if (regionflag == 0) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) values_one[bin[i]][m] += rmass[i];
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else values_one[bin[i]][m] += mass[type[i]];
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}
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass) values_one[bin[i]][m] += rmass[i];
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else values_one[bin[i]][m] += mass[type[i]];
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}
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} else {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
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if (rmass) values_one[bin[i]][m] += rmass[i];
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else values_one[bin[i]][m] += mass[type[i]];
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}
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
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if (rmass) values_one[bin[i]][m] += rmass[i];
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else values_one[bin[i]][m] += mass[type[i]];
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}
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}
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// COMPUTE adds its scalar or vector component to values
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@ -605,25 +605,25 @@ void FixAveSpatial::end_of_step()
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} else if (which[m] == COMPUTE) {
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Compute *compute = modify->compute[n];
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if (!(compute->invoked_flag & INVOKED_PERATOM)) {
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compute->compute_peratom();
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compute->invoked_flag |= INVOKED_PERATOM;
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compute->compute_peratom();
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compute->invoked_flag |= INVOKED_PERATOM;
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}
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double *vector = compute->vector_atom;
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double **array = compute->array_atom;
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int jm1 = j - 1;
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if (regionflag == 0) {
|
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for (i = 0; i < nlocal; i++)
|
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if (mask[i] & groupbit) {
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if (j == 0) values_one[bin[i]][m] += vector[i];
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else values_one[bin[i]][m] += array[i][jm1];
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}
|
||||
for (i = 0; i < nlocal; i++)
|
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if (mask[i] & groupbit) {
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if (j == 0) values_one[bin[i]][m] += vector[i];
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else values_one[bin[i]][m] += array[i][jm1];
|
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}
|
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} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
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if (j == 0) values_one[bin[i]][m] += vector[i];
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else values_one[bin[i]][m] += array[i][jm1];
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}
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
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if (j == 0) values_one[bin[i]][m] += vector[i];
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else values_one[bin[i]][m] += array[i][jm1];
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}
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}
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// FIX adds its scalar or vector component to values
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@ -635,17 +635,17 @@ void FixAveSpatial::end_of_step()
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int jm1 = j - 1;
|
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|
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if (regionflag == 0) {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (j == 0) values_one[bin[i]][m] += vector[i];
|
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else values_one[bin[i]][m] += array[i][jm1];
|
||||
}
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
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if (j == 0) values_one[bin[i]][m] += vector[i];
|
||||
else values_one[bin[i]][m] += array[i][jm1];
|
||||
}
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
if (j == 0) values_one[bin[i]][m] += vector[i];
|
||||
else values_one[bin[i]][m] += array[i][jm1];
|
||||
}
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
if (j == 0) values_one[bin[i]][m] += vector[i];
|
||||
else values_one[bin[i]][m] += array[i][jm1];
|
||||
}
|
||||
}
|
||||
|
||||
// VARIABLE adds its per-atom quantities to values
|
||||
@ -653,21 +653,21 @@ void FixAveSpatial::end_of_step()
|
||||
|
||||
} else if (which[m] == VARIABLE) {
|
||||
if (nlocal > maxvar) {
|
||||
maxvar = atom->nmax;
|
||||
memory->destroy(varatom);
|
||||
memory->create(varatom,maxvar,"ave/spatial:varatom");
|
||||
maxvar = atom->nmax;
|
||||
memory->destroy(varatom);
|
||||
memory->create(varatom,maxvar,"ave/spatial:varatom");
|
||||
}
|
||||
|
||||
input->variable->compute_atom(n,igroup,varatom,1,0);
|
||||
|
||||
if (regionflag == 0) {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
values_one[bin[i]][m] += varatom[i];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
values_one[bin[i]][m] += varatom[i];
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
|
||||
values_one[bin[i]][m] += varatom[i];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2]))
|
||||
values_one[bin[i]][m] += varatom[i];
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -681,17 +681,17 @@ void FixAveSpatial::end_of_step()
|
||||
for (m = 0; m < nbins; m++) {
|
||||
count_many[m] += count_one[m];
|
||||
for (j = 0; j < nvalues; j++)
|
||||
values_many[m][j] += values_one[m][j];
|
||||
values_many[m][j] += values_one[m][j];
|
||||
}
|
||||
} else {
|
||||
MPI_Allreduce(count_one,count_many,nbins,MPI_DOUBLE,MPI_SUM,world);
|
||||
for (m = 0; m < nbins; m++) {
|
||||
if (count_many[m] > 0.0)
|
||||
for (j = 0; j < nvalues; j++) {
|
||||
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
|
||||
values_many[m][j] += values_one[m][j];
|
||||
else values_many[m][j] += values_one[m][j]/count_many[m];
|
||||
}
|
||||
for (j = 0; j < nvalues; j++) {
|
||||
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
|
||||
values_many[m][j] += values_one[m][j];
|
||||
else values_many[m][j] += values_one[m][j]/count_many[m];
|
||||
}
|
||||
count_sum[m] += count_many[m];
|
||||
}
|
||||
}
|
||||
@ -721,21 +721,21 @@ void FixAveSpatial::end_of_step()
|
||||
if (normflag == ALL) {
|
||||
MPI_Allreduce(count_many,count_sum,nbins,MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues,
|
||||
MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_DOUBLE,MPI_SUM,world);
|
||||
for (m = 0; m < nbins; m++) {
|
||||
if (count_sum[m] > 0.0)
|
||||
for (j = 0; j < nvalues; j++)
|
||||
if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat;
|
||||
else if (which[j] == DENSITY_MASS) values_sum[m][j] *= mv2d/repeat;
|
||||
else values_sum[m][j] /= count_sum[m];
|
||||
for (j = 0; j < nvalues; j++)
|
||||
if (which[j] == DENSITY_NUMBER) values_sum[m][j] /= repeat;
|
||||
else if (which[j] == DENSITY_MASS) values_sum[m][j] *= mv2d/repeat;
|
||||
else values_sum[m][j] /= count_sum[m];
|
||||
count_sum[m] /= repeat;
|
||||
}
|
||||
} else {
|
||||
MPI_Allreduce(&values_many[0][0],&values_sum[0][0],nbins*nvalues,
|
||||
MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_DOUBLE,MPI_SUM,world);
|
||||
for (m = 0; m < nbins; m++) {
|
||||
for (j = 0; j < nvalues; j++)
|
||||
values_sum[m][j] /= repeat;
|
||||
values_sum[m][j] /= repeat;
|
||||
count_sum[m] /= repeat;
|
||||
}
|
||||
}
|
||||
@ -745,7 +745,7 @@ void FixAveSpatial::end_of_step()
|
||||
for (j = 0; j < nvalues; j++)
|
||||
if (which[j] == DENSITY_NUMBER || which[j] == DENSITY_MASS)
|
||||
for (m = 0; m < nbins; m++)
|
||||
values_sum[m][j] /= bin_volume;
|
||||
values_sum[m][j] /= bin_volume;
|
||||
|
||||
// if ave = ONE, only single Nfreq timestep value is needed
|
||||
// if ave = RUNNING, combine with all previous Nfreq timestep values
|
||||
@ -753,8 +753,8 @@ void FixAveSpatial::end_of_step()
|
||||
|
||||
if (ave == ONE) {
|
||||
for (m = 0; m < nbins; m++) {
|
||||
for (i = 0; i < nvalues; i++)
|
||||
values_total[m][i] = values_sum[m][i];
|
||||
for (i = 0; i < nvalues; i++)
|
||||
values_total[m][i] = values_sum[m][i];
|
||||
count_total[m] = count_sum[m];
|
||||
}
|
||||
norm = 1;
|
||||
@ -762,7 +762,7 @@ void FixAveSpatial::end_of_step()
|
||||
} else if (ave == RUNNING) {
|
||||
for (m = 0; m < nbins; m++) {
|
||||
for (i = 0; i < nvalues; i++)
|
||||
values_total[m][i] += values_sum[m][i];
|
||||
values_total[m][i] += values_sum[m][i];
|
||||
count_total[m] += count_sum[m];
|
||||
}
|
||||
norm++;
|
||||
@ -770,9 +770,9 @@ void FixAveSpatial::end_of_step()
|
||||
} else if (ave == WINDOW) {
|
||||
for (m = 0; m < nbins; m++) {
|
||||
for (i = 0; i < nvalues; i++) {
|
||||
values_total[m][i] += values_sum[m][i];
|
||||
if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
|
||||
values_list[iwindow][m][i] = values_sum[m][i];
|
||||
values_total[m][i] += values_sum[m][i];
|
||||
if (window_limit) values_total[m][i] -= values_list[iwindow][m][i];
|
||||
values_list[iwindow][m][i] = values_sum[m][i];
|
||||
}
|
||||
count_total[m] += count_sum[m];
|
||||
if (window_limit) count_total[m] -= count_list[iwindow][m];
|
||||
@ -789,32 +789,32 @@ void FixAveSpatial::end_of_step()
|
||||
}
|
||||
|
||||
// output result to file
|
||||
|
||||
|
||||
if (fp && me == 0) {
|
||||
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nbins);
|
||||
if (ndim == 1)
|
||||
for (m = 0; m < nbins; m++) {
|
||||
fprintf(fp," %d %g %g",m+1,coord[m][0],
|
||||
count_total[m]/norm);
|
||||
for (i = 0; i < nvalues; i++)
|
||||
fprintf(fp," %g",values_total[m][i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
fprintf(fp," %d %g %g",m+1,coord[m][0],
|
||||
count_total[m]/norm);
|
||||
for (i = 0; i < nvalues; i++)
|
||||
fprintf(fp," %g",values_total[m][i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
else if (ndim == 2)
|
||||
for (m = 0; m < nbins; m++) {
|
||||
fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1],
|
||||
count_total[m]/norm);
|
||||
for (i = 0; i < nvalues; i++)
|
||||
fprintf(fp," %g",values_total[m][i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
fprintf(fp," %d %g %g %g",m+1,coord[m][0],coord[m][1],
|
||||
count_total[m]/norm);
|
||||
for (i = 0; i < nvalues; i++)
|
||||
fprintf(fp," %g",values_total[m][i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
else
|
||||
for (m = 0; m < nbins; m++) {
|
||||
fprintf(fp," %d %g %g %g %g",m+1,coord[m][0],coord[m][1],coord[m][2],
|
||||
count_total[m]/norm);
|
||||
for (i = 0; i < nvalues; i++)
|
||||
fprintf(fp," %g",values_total[m][i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
fprintf(fp," %d %g %g %g %g",m+1,coord[m][0],coord[m][1],coord[m][2],
|
||||
count_total[m]/norm);
|
||||
for (i = 0; i < nvalues; i++)
|
||||
fprintf(fp," %g",values_total[m][i]/norm);
|
||||
fprintf(fp,"\n");
|
||||
}
|
||||
|
||||
fflush(fp);
|
||||
@ -854,9 +854,9 @@ void FixAveSpatial::setup_bins()
|
||||
for (m = 0; m < ndim; m++) {
|
||||
if (originflag[m] == LOWER) origin[m] = boxlo[dim[m]];
|
||||
else if (originflag[m] == UPPER) origin[m] = boxhi[dim[m]];
|
||||
else if (originflag[m] == CENTER)
|
||||
else if (originflag[m] == CENTER)
|
||||
origin[m] = 0.5 * (boxlo[dim[m]] + boxhi[dim[m]]);
|
||||
|
||||
|
||||
if (origin[m] < boxlo[dim[m]]) {
|
||||
n = static_cast<int> ((boxlo[dim[m]] - origin[m]) * invdelta[m]);
|
||||
lo = origin[m] + n*delta[m];
|
||||
@ -873,7 +873,7 @@ void FixAveSpatial::setup_bins()
|
||||
n = static_cast<int> ((origin[m] - boxhi[dim[m]]) * invdelta[m]);
|
||||
hi = origin[m] - n*delta[m];
|
||||
}
|
||||
|
||||
|
||||
offset[m] = lo;
|
||||
nlayers[m] = static_cast<int> ((hi-lo) * invdelta[m] + 0.5);
|
||||
nbins *= nlayers[m];
|
||||
@ -888,19 +888,19 @@ void FixAveSpatial::setup_bins()
|
||||
memory->grow(count_many,nbins,"ave/spatial:count_many");
|
||||
memory->grow(count_sum,nbins,"ave/spatial:count_sum");
|
||||
memory->grow(count_total,nbins,"ave/spatial:count_total");
|
||||
|
||||
|
||||
memory->grow(coord,nbins,ndim,"ave/spatial:coord");
|
||||
memory->grow(values_one,nbins,nvalues,"ave/spatial:values_one");
|
||||
memory->grow(values_many,nbins,nvalues,"ave/spatial:values_many");
|
||||
memory->grow(values_sum,nbins,nvalues,"ave/spatial:values_sum");
|
||||
memory->grow(values_total,nbins,nvalues,"ave/spatial:values_total");
|
||||
|
||||
|
||||
// only allocate count and values list for ave = WINDOW
|
||||
|
||||
|
||||
if (ave == WINDOW) {
|
||||
memory->create(count_list,nwindow,nbins,"ave/spatial:count_list");
|
||||
memory->create(values_list,nwindow,nbins,nvalues,
|
||||
"ave/spatial:values_list");
|
||||
"ave/spatial:values_list");
|
||||
}
|
||||
|
||||
// reinitialize regrown count/values total since they accumulate
|
||||
@ -921,9 +921,9 @@ void FixAveSpatial::setup_bins()
|
||||
for (i = 0; i < nlayers[0]; i++) {
|
||||
coord1 = offset[0] + (i+0.5)*delta[0];
|
||||
for (j = 0; j < nlayers[1]; j++) {
|
||||
coord[m][0] = coord1;
|
||||
coord[m][1] = offset[1] + (j+0.5)*delta[1];
|
||||
m++;
|
||||
coord[m][0] = coord1;
|
||||
coord[m][1] = offset[1] + (j+0.5)*delta[1];
|
||||
m++;
|
||||
}
|
||||
}
|
||||
} else if (ndim == 3) {
|
||||
@ -931,13 +931,13 @@ void FixAveSpatial::setup_bins()
|
||||
for (i = 0; i < nlayers[0]; i++) {
|
||||
coord1 = offset[0] + (i+0.5)*delta[0];
|
||||
for (j = 0; j < nlayers[1]; j++) {
|
||||
coord2 = offset[1] + (j+0.5)*delta[1];
|
||||
for (k = 0; k < nlayers[2]; k++) {
|
||||
coord[m][0] = coord1;
|
||||
coord[m][1] = coord2;
|
||||
coord[m][2] = offset[2] + (k+0.5)*delta[2];
|
||||
m++;
|
||||
}
|
||||
coord2 = offset[1] + (j+0.5)*delta[1];
|
||||
for (k = 0; k < nlayers[2]; k++) {
|
||||
coord[m][0] = coord1;
|
||||
coord[m][1] = coord2;
|
||||
coord[m][2] = offset[2] + (k+0.5)*delta[2];
|
||||
m++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -981,35 +981,35 @@ void FixAveSpatial::atom2bin1d()
|
||||
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xremap = x[i][idim];
|
||||
if (periodicity) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
ibin = MAX(ibin,0);
|
||||
ibin = MIN(ibin,nlayerm1);
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
xremap = x[i][idim];
|
||||
if (periodicity) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
ibin = MAX(ibin,0);
|
||||
ibin = MIN(ibin,nlayerm1);
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
}
|
||||
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
|
||||
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
if (scaleflag == REDUCED) {
|
||||
domain->x2lamda(x[i],lamda);
|
||||
xremap = lamda[idim];
|
||||
} else xremap = x[i][idim];
|
||||
if (periodicity) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
ibin = MAX(ibin,0);
|
||||
ibin = MIN(ibin,nlayerm1);
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
if (scaleflag == REDUCED) {
|
||||
domain->x2lamda(x[i],lamda);
|
||||
xremap = lamda[idim];
|
||||
} else xremap = x[i][idim];
|
||||
if (periodicity) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
ibin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
ibin = MAX(ibin,0);
|
||||
ibin = MIN(ibin,nlayerm1);
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1054,61 +1054,61 @@ void FixAveSpatial::atom2bin2d()
|
||||
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xremap = x[i][idim];
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1);
|
||||
xremap = x[i][idim];
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1);
|
||||
|
||||
yremap = x[i][jdim];
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1);
|
||||
yremap = x[i][jdim];
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1);
|
||||
|
||||
ibin = i1bin*nlayers[1] + i2bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
ibin = i1bin*nlayers[1] + i2bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
}
|
||||
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
|
||||
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
if (scaleflag == REDUCED) {
|
||||
domain->x2lamda(x[i],lamda);
|
||||
xremap = lamda[idim];
|
||||
yremap = lamda[jdim];
|
||||
} else {
|
||||
xremap = x[i][idim];
|
||||
yremap = x[i][jdim];
|
||||
}
|
||||
if (scaleflag == REDUCED) {
|
||||
domain->x2lamda(x[i],lamda);
|
||||
xremap = lamda[idim];
|
||||
yremap = lamda[jdim];
|
||||
} else {
|
||||
xremap = x[i][idim];
|
||||
yremap = x[i][jdim];
|
||||
}
|
||||
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1-1);
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1-1);
|
||||
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1-1);
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1-1);
|
||||
|
||||
ibin = i1bin*nlayers[1] + i2bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
ibin = i1bin*nlayers[1] + i2bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -1155,80 +1155,80 @@ void FixAveSpatial::atom2bin3d()
|
||||
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
xremap = x[i][idim];
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1);
|
||||
xremap = x[i][idim];
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1);
|
||||
|
||||
yremap = x[i][jdim];
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1);
|
||||
yremap = x[i][jdim];
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1);
|
||||
|
||||
zremap = x[i][kdim];
|
||||
if (periodicity[kdim]) {
|
||||
if (zremap < boxlo[kdim]) yremap += prd[kdim];
|
||||
if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
|
||||
}
|
||||
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
|
||||
i3bin = MAX(i3bin,0);
|
||||
i3bin = MIN(i3bin,nlayer3m1);
|
||||
zremap = x[i][kdim];
|
||||
if (periodicity[kdim]) {
|
||||
if (zremap < boxlo[kdim]) yremap += prd[kdim];
|
||||
if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
|
||||
}
|
||||
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
|
||||
i3bin = MAX(i3bin,0);
|
||||
i3bin = MIN(i3bin,nlayer3m1);
|
||||
|
||||
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
}
|
||||
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
|
||||
|
||||
} else {
|
||||
for (i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
|
||||
if (scaleflag == REDUCED) {
|
||||
domain->x2lamda(x[i],lamda);
|
||||
xremap = lamda[idim];
|
||||
yremap = lamda[jdim];
|
||||
zremap = lamda[kdim];
|
||||
} else {
|
||||
xremap = x[i][idim];
|
||||
yremap = x[i][jdim];
|
||||
zremap = x[i][kdim];
|
||||
}
|
||||
if (scaleflag == REDUCED) {
|
||||
domain->x2lamda(x[i],lamda);
|
||||
xremap = lamda[idim];
|
||||
yremap = lamda[jdim];
|
||||
zremap = lamda[kdim];
|
||||
} else {
|
||||
xremap = x[i][idim];
|
||||
yremap = x[i][jdim];
|
||||
zremap = x[i][kdim];
|
||||
}
|
||||
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1);
|
||||
if (periodicity[idim]) {
|
||||
if (xremap < boxlo[idim]) xremap += prd[idim];
|
||||
if (xremap >= boxhi[idim]) xremap -= prd[idim];
|
||||
}
|
||||
i1bin = static_cast<int> ((xremap - offset[0]) * invdelta[0]);
|
||||
i1bin = MAX(i1bin,0);
|
||||
i1bin = MIN(i1bin,nlayer1m1);
|
||||
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1);
|
||||
if (periodicity[jdim]) {
|
||||
if (yremap < boxlo[jdim]) yremap += prd[jdim];
|
||||
if (yremap >= boxhi[jdim]) yremap -= prd[jdim];
|
||||
}
|
||||
i2bin = static_cast<int> ((yremap - offset[1]) * invdelta[1]);
|
||||
i2bin = MAX(i2bin,0);
|
||||
i2bin = MIN(i2bin,nlayer2m1);
|
||||
|
||||
if (periodicity[kdim]) {
|
||||
if (zremap < boxlo[kdim]) yremap += prd[kdim];
|
||||
if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
|
||||
}
|
||||
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
|
||||
i3bin = MAX(i3bin,0);
|
||||
i3bin = MIN(i3bin,nlayer3m1);
|
||||
if (periodicity[kdim]) {
|
||||
if (zremap < boxlo[kdim]) yremap += prd[kdim];
|
||||
if (zremap >= boxhi[kdim]) yremap -= prd[kdim];
|
||||
}
|
||||
i3bin = static_cast<int> ((zremap - offset[2]) * invdelta[2]);
|
||||
i3bin = MAX(i3bin,0);
|
||||
i3bin = MIN(i3bin,nlayer3m1);
|
||||
|
||||
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
ibin = i1bin*nlayers[1]*nlayers[2] + i2bin*nlayers[2] + i3bin;
|
||||
bin[i] = ibin;
|
||||
count_one[ibin] += 1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user