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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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112
src/fix_ave_atom.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -86,9 +86,9 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
which[nvalues] = F;
argindex[nvalues++] = 2;
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
} else if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
@ -99,10 +99,10 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/atom command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/atom command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@ -128,41 +128,41 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/atom does not exist");
error->all(FLERR,"Compute ID for fix ave/atom does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all(FLERR,"Fix ave/atom compute does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Fix ave/atom compute does not "
"calculate a per-atom vector");
error->all(FLERR,"Fix ave/atom compute does not calculate per-atom values");
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Fix ave/atom compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Fix ave/atom compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range");
error->all(FLERR,"Fix ave/atom compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,"Fix ave/atom compute array is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/atom does not exist");
error->all(FLERR,"Fix ID for fix ave/atom does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values");
error->all(FLERR,"Fix ave/atom fix does not calculate per-atom values");
if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom vector");
error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom array");
error->all(FLERR,"Fix ave/atom fix does not calculate a per-atom array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range");
error->all(FLERR,"Fix ave/atom fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->peratom_freq)
error->all(FLERR,"Fix for fix ave/atom not computed at compatible time");
error->all(FLERR,"Fix for fix ave/atom not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/atom does not exist");
error->all(FLERR,"Variable name for fix ave/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Fix ave/atom variable is not atom-style variable");
error->all(FLERR,"Fix ave/atom variable is not atom-style variable");
}
}
@ -186,7 +186,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < nvalues; m++)
array[i][m] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
@ -202,7 +202,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
FixAveAtom::~FixAveAtom()
{
// unregister callback to this fix from Atom class
atom->delete_callback(id,0);
delete [] which;
@ -233,19 +233,19 @@ void FixAveAtom::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/atom does not exist");
error->all(FLERR,"Compute ID for fix ave/atom does not exist");
value2index[m] = icompute;
} else if (which[m] == FIX) {
int ifix = modify->find_fix(ids[m]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/atom does not exist");
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/atom does not exist");
value2index[m] = ifix;
} else if (which[m] == VARIABLE) {
int ivariable = input->variable->find(ids[m]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/atom does not exist");
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/atom does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@ -287,8 +287,8 @@ void FixAveAtom::end_of_step()
if (irepeat == 0)
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
array[i][m] = 0.0;
array[i][m] = 0.0;
// accumulate results of attributes,computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
@ -303,50 +303,50 @@ void FixAveAtom::end_of_step()
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += x[i][j];
if (mask[i] & groupbit) array[i][m] += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += v[i][j];
if (mask[i] & groupbit) array[i][m] += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += f[i][j];
if (mask[i] & groupbit) array[i][m] += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (j == 0) {
double *compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += compute_vector[i];
double *compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += compute_vector[i];
} else {
int jm1 = j - 1;
double **compute_array = compute->array_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
int jm1 = j - 1;
double **compute_array = compute->array_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
}
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
if (j == 0) {
double *fix_vector = modify->fix[n]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += fix_vector[i];
double *fix_vector = modify->fix[n]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += fix_vector[i];
} else {
int jm1 = j - 1;
double **fix_array = modify->fix[n]->array_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
int jm1 = j - 1;
double **fix_array = modify->fix[n]->array_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
}
// evaluate atom-style variable