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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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This commit is contained in:
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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164
src/compute_slice.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.
@ -53,8 +53,8 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
nvalues = 0;
for (int iarg = 6; iarg < narg; iarg++) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
@ -64,10 +64,10 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal compute slice command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal compute slice command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@ -85,39 +85,39 @@ ComputeSlice::ComputeSlice(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 compute slice does not exist");
error->all(FLERR,"Compute ID for compute slice does not exist");
if (modify->compute[icompute]->vector_flag) {
if (argindex[i])
error->all(FLERR,"Compute slice compute does not calculate a global array");
if (nstop > modify->compute[icompute]->size_vector)
error->all(FLERR,"Compute slice compute vector is accessed out-of-range");
if (argindex[i])
error->all(FLERR,"Compute slice compute does not calculate a global array");
if (nstop > modify->compute[icompute]->size_vector)
error->all(FLERR,"Compute slice compute vector is accessed out-of-range");
} else if (modify->compute[icompute]->array_flag) {
if (argindex[i] == 0)
error->all(FLERR,"Compute slice compute does not calculate a global vector");
if (argindex[i] > modify->compute[icompute]->size_array_cols)
error->all(FLERR,"Compute slice compute array is accessed out-of-range");
if (nstop > modify->compute[icompute]->size_array_rows)
error->all(FLERR,"Compute slice compute array is accessed out-of-range");
if (argindex[i] == 0)
error->all(FLERR,"Compute slice compute does not calculate a global vector");
if (argindex[i] > modify->compute[icompute]->size_array_cols)
error->all(FLERR,"Compute slice compute array is accessed out-of-range");
if (nstop > modify->compute[icompute]->size_array_rows)
error->all(FLERR,"Compute slice compute array is accessed out-of-range");
} else error->all(FLERR,"Compute slice compute does not calculate "
"global vector or array");
"global vector or array");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute slice does not exist");
error->all(FLERR,"Fix ID for compute slice does not exist");
if (modify->fix[ifix]->vector_flag) {
if (argindex[i])
error->all(FLERR,"Compute slice fix does not calculate a global array");
if (nstop > modify->fix[ifix]->size_vector)
error->all(FLERR,"Compute slice fix vector is accessed out-of-range");
if (argindex[i])
error->all(FLERR,"Compute slice fix does not calculate a global array");
if (nstop > modify->fix[ifix]->size_vector)
error->all(FLERR,"Compute slice fix vector is accessed out-of-range");
} else if (modify->fix[ifix]->array_flag) {
if (argindex[i] == 0)
error->all(FLERR,"Compute slice fix does not calculate a global vector");
if (argindex[i] > modify->fix[ifix]->size_array_cols)
error->all(FLERR,"Compute slice fix array is accessed out-of-range");
if (nstop > modify->fix[ifix]->size_array_rows)
error->all(FLERR,"Compute slice fix array is accessed out-of-range");
if (argindex[i] == 0)
error->all(FLERR,"Compute slice fix does not calculate a global vector");
if (argindex[i] > modify->fix[ifix]->size_array_cols)
error->all(FLERR,"Compute slice fix array is accessed out-of-range");
if (nstop > modify->fix[ifix]->size_array_rows)
error->all(FLERR,"Compute slice fix array is accessed out-of-range");
} else error->all(FLERR,"Compute slice fix does not calculate "
"global vector or array");
"global vector or array");
}
}
@ -137,24 +137,24 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
if (which[0] == COMPUTE) {
int icompute = modify->find_compute(ids[0]);
if (argindex[0] == 0) {
extvector = modify->compute[icompute]->extvector;
if (modify->compute[icompute]->extvector == -1) {
extlist = new int[size_vector];
int j = 0;
for (int i = nstart; i < nstop; i += nskip)
extlist[j++] = modify->compute[icompute]->extlist[i-1];
}
extvector = modify->compute[icompute]->extvector;
if (modify->compute[icompute]->extvector == -1) {
extlist = new int[size_vector];
int j = 0;
for (int i = nstart; i < nstop; i += nskip)
extlist[j++] = modify->compute[icompute]->extlist[i-1];
}
} else extvector = modify->compute[icompute]->extarray;
} else if (which[0] == FIX) {
int ifix = modify->find_fix(ids[0]);
if (argindex[0] == 0) {
extvector = modify->fix[ifix]->extvector;
if (modify->fix[ifix]->extvector == -1) {
extlist = new int[size_vector];
int j = 0;
for (int i = nstart; i < nstop; i += nskip)
extlist[j++] = modify->fix[ifix]->extlist[i-1];
}
extvector = modify->fix[ifix]->extvector;
if (modify->fix[ifix]->extvector == -1) {
extlist = new int[size_vector];
int j = 0;
for (int i = nstart; i < nstop; i += nskip)
extlist[j++] = modify->fix[ifix]->extlist[i-1];
}
} else extvector = modify->fix[ifix]->extarray;
}
@ -167,27 +167,27 @@ ComputeSlice::ComputeSlice(LAMMPS *lmp, int narg, char **arg) :
extarray = 0;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (argindex[i] == 0) {
if (modify->compute[icompute]->extvector == 1) extarray = 1;
if (modify->compute[icompute]->extvector == -1) {
for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
if (modify->compute[icompute]->extlist[j]) extarray = 1;
}
} else {
if (modify->compute[icompute]->extarray) extarray = 1;
}
int icompute = modify->find_compute(ids[i]);
if (argindex[i] == 0) {
if (modify->compute[icompute]->extvector == 1) extarray = 1;
if (modify->compute[icompute]->extvector == -1) {
for (int j = 0; j < modify->compute[icompute]->size_vector; j++)
if (modify->compute[icompute]->extlist[j]) extarray = 1;
}
} else {
if (modify->compute[icompute]->extarray) extarray = 1;
}
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (argindex[i] == 0) {
if (modify->fix[ifix]->extvector == 1) extarray = 1;
if (modify->fix[ifix]->extvector == -1) {
for (int j = 0; j < modify->fix[ifix]->size_vector; j++)
if (modify->fix[ifix]->extlist[j]) extarray = 1;
}
} else {
if (modify->fix[ifix]->extarray) extarray = 1;
}
int ifix = modify->find_fix(ids[i]);
if (argindex[i] == 0) {
if (modify->fix[ifix]->extvector == 1) extarray = 1;
if (modify->fix[ifix]->extvector == -1) {
for (int j = 0; j < modify->fix[ifix]->size_vector; j++)
if (modify->fix[ifix]->extlist[j]) extarray = 1;
}
} else {
if (modify->fix[ifix]->extarray) extarray = 1;
}
}
}
}
@ -217,12 +217,12 @@ void ComputeSlice::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute slice does not exist");
error->all(FLERR,"Compute ID for compute slice 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 compute slice does not exist");
if (ifix < 0)
error->all(FLERR,"Fix ID for compute slice does not exist");
value2index[m] = ifix;
}
}
@ -263,32 +263,32 @@ void ComputeSlice::extract_one(int m, double *vec, int stride)
if (argindex[m] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = cvector[i-1];
j += stride;
vec[j] = cvector[i-1];
j += stride;
}
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = carray[i-1][icol];
j += stride;
vec[j] = carray[i-1][icol];
j += stride;
}
}
// access fix fields, check if fix frequency is a match
} else if (which[m] == FIX) {
if (update->ntimestep % modify->fix[value2index[m]]->global_freq)
error->all(FLERR,"Fix used in compute slice not computed at compatible time");
@ -297,15 +297,15 @@ void ComputeSlice::extract_one(int m, double *vec, int stride)
if (argindex[m] == 0) {
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_vector(i-1);
j += stride;
vec[j] = fix->compute_vector(i-1);
j += stride;
}
} else {
int icol = argindex[m]-1;
j = 0;
for (i = nstart; i < nstop; i += nskip) {
vec[j] = fix->compute_array(i-1,icol);
j += stride;
vec[j] = fix->compute_array(i-1,icol);
j += stride;
}
}
}