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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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308
src/compute_reduce.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.
@ -112,9 +112,9 @@ ComputeReduce::ComputeReduce(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;
@ -125,10 +125,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal compute reduce command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal compute reduce command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
@ -151,14 +151,14 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
if (strcmp(arg[iarg],"replace") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal compute reduce command");
if (mode != MINN && mode != MAXX)
error->all(FLERR,"Compute reduce replace requires min or max mode");
error->all(FLERR,"Compute reduce replace requires min or max mode");
int col1 = atoi(arg[iarg+1]) - 1;
int col2 = atoi(arg[iarg+2]) - 1;
if (col1 < 0 || col1 >= nvalues || col2 < 0 || col2 >= nvalues)
error->all(FLERR,"Illegal compute reduce command");
if (col1 == col2) error->all(FLERR,"Illegal compute reduce command");
error->all(FLERR,"Illegal compute reduce command");
if (col1 == col2) error->all(FLERR,"Illegal compute reduce command");
if (replace[col1] >= 0 || replace[col2] >= 0)
error->all(FLERR,"Invalid replace values in compute reduce");
error->all(FLERR,"Invalid replace values in compute reduce");
replace[col1] = col2;
iarg += 3;
} else error->all(FLERR,"Illegal compute reduce command");
@ -183,69 +183,69 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) :
else if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute reduce does not exist");
error->all(FLERR,"Compute ID for compute reduce does not exist");
if (modify->compute[icompute]->peratom_flag) {
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a per-atom vector");
if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_peratom_cols)
error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
} else if (modify->compute[icompute]->local_flag) {
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_local_cols != 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_local_cols)
error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->compute[icompute]->size_local_cols != 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a local vector");
if (argindex[i] && modify->compute[icompute]->size_local_cols == 0)
error->all(FLERR,"Compute reduce compute does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_local_cols)
error->all(FLERR,"Compute reduce compute array is accessed out-of-range");
} else error->all(FLERR,"Compute reduce compute calculates global values");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for compute reduce does not exist");
error->all(FLERR,"Fix ID for compute reduce does not exist");
if (modify->fix[ifix]->peratom_flag) {
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
flavor[i] = PERATOM;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_peratom_cols != 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a per-atom vector");
if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a per-atom array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_peratom_cols)
error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
} else if (modify->fix[ifix]->local_flag) {
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_local_cols != 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_local_cols)
error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
flavor[i] = LOCAL;
if (argindex[i] == 0 &&
modify->fix[ifix]->size_local_cols != 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a local vector");
if (argindex[i] && modify->fix[ifix]->size_local_cols == 0)
error->all(FLERR,"Compute reduce fix does not "
"calculate a local array");
if (argindex[i] &&
argindex[i] > modify->fix[ifix]->size_local_cols)
error->all(FLERR,"Compute reduce fix array is accessed out-of-range");
} else error->all(FLERR,"Compute reduce fix calculates global values");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for compute reduce does not exist");
error->all(FLERR,"Variable name for compute reduce does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all(FLERR,"Compute reduce variable is not atom-style variable");
error->all(FLERR,"Compute reduce variable is not atom-style variable");
flavor[i] = PERATOM;
}
}
@ -304,19 +304,19 @@ void ComputeReduce::init()
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all(FLERR,"Compute ID for compute reduce does not exist");
error->all(FLERR,"Compute ID for compute reduce 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 reduce does not exist");
if (ifix < 0)
error->all(FLERR,"Fix ID for compute reduce 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 compute reduce does not exist");
if (ivariable < 0)
error->all(FLERR,"Variable name for compute reduce does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
@ -373,45 +373,45 @@ void ComputeReduce::compute_vector()
} else if (mode == MINN) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MIN,world);
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MIN,world);
} else {
for (int m = 0; m < nvalues; m++)
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MINLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
for (int m = 0; m < nvalues; m++)
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
}
} else if (mode == MAXX) {
if (!replace) {
for (int m = 0; m < nvalues; m++)
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MAX,world);
MPI_Allreduce(&onevec[m],&vector[m],1,MPI_DOUBLE,MPI_MAX,world);
} else {
for (int m = 0; m < nvalues; m++)
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
if (replace[m] < 0) {
pairme.value = onevec[m];
pairme.proc = me;
MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world);
vector[m] = pairall.value;
owner[m] = pairall.proc;
}
for (int m = 0; m < nvalues; m++)
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
if (replace[m] >= 0) {
if (me == owner[replace[m]])
vector[m] = compute_one(m,indices[replace[m]]);
MPI_Bcast(&vector[m],1,MPI_DOUBLE,owner[replace[m]],world);
}
}
} else if (mode == AVE) {
@ -457,70 +457,70 @@ double ComputeReduce::compute_one(int m, int flag)
double **x = atom->x;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,x[i][aidx],i);
if (mask[i] & groupbit) combine(one,x[i][aidx],i);
} else one = x[flag][aidx];
} else if (which[m] == V) {
double **v = atom->v;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,v[i][aidx],i);
if (mask[i] & groupbit) combine(one,v[i][aidx],i);
} else one = v[flag][aidx];
} else if (which[m] == F) {
double **f = atom->f;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,f[i][aidx],i);
if (mask[i] & groupbit) combine(one,f[i][aidx],i);
} else one = f[flag][aidx];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[vidx];
if (flavor[m] == PERATOM) {
if (!(compute->invoked_flag & INVOKED_PERATOM)) {
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
compute->compute_peratom();
compute->invoked_flag |= INVOKED_PERATOM;
}
if (aidx == 0) {
double *comp_vec = compute->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,comp_vec[i],i);
} else one = comp_vec[flag];
double *comp_vec = compute->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,comp_vec[i],i);
} else one = comp_vec[flag];
} else {
double **carray_atom = compute->array_atom;
int n = nlocal;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i);
} else one = carray_atom[flag][aidxm1];
double **carray_atom = compute->array_atom;
int n = nlocal;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,carray_atom[i][aidxm1],i);
} else one = carray_atom[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (!(compute->invoked_flag & INVOKED_LOCAL)) {
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
compute->compute_local();
compute->invoked_flag |= INVOKED_LOCAL;
}
if (aidx == 0) {
double *comp_vec = compute->vector_local;
int n = compute->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,comp_vec[i],i);
else one = comp_vec[flag];
double *comp_vec = compute->vector_local;
int n = compute->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,comp_vec[i],i);
else one = comp_vec[flag];
} else {
double **carray_local = compute->array_local;
int n = compute->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,carray_local[i][aidxm1],i);
else one = carray_local[flag][aidxm1];
double **carray_local = compute->array_local;
int n = compute->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,carray_local[i][aidxm1],i);
else one = carray_local[flag][aidxm1];
}
}
@ -533,40 +533,40 @@ double ComputeReduce::compute_one(int m, int flag)
if (flavor[m] == PERATOM) {
if (aidx == 0) {
double *fix_vector = fix->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,fix_vector[i],i);
} else one = fix_vector[flag];
double *fix_vector = fix->vector_atom;
int n = nlocal;
if (flag < 0) {
for (i = 0; i < n; i++)
if (mask[i] & groupbit) combine(one,fix_vector[i],i);
} else one = fix_vector[flag];
} else {
double **fix_array = fix->array_atom;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i);
} else one = fix_array[flag][aidxm1];
double **fix_array = fix->array_atom;
int aidxm1 = aidx - 1;
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,fix_array[i][aidxm1],i);
} else one = fix_array[flag][aidxm1];
}
} else if (flavor[m] == LOCAL) {
if (aidx == 0) {
double *fix_vector = fix->vector_local;
int n = fix->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_vector[i],i);
else one = fix_vector[flag];
double *fix_vector = fix->vector_local;
int n = fix->size_local_rows;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_vector[i],i);
else one = fix_vector[flag];
} else {
double **fix_array = fix->array_local;
int n = fix->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_array[i][aidxm1],i);
else one = fix_array[flag][aidxm1];
double **fix_array = fix->array_local;
int n = fix->size_local_rows;
int aidxm1 = aidx - 1;
if (flag < 0)
for (i = 0; i < n; i++)
combine(one,fix_array[i][aidxm1],i);
else one = fix_array[flag][aidxm1];
}
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE) {
@ -579,7 +579,7 @@ double ComputeReduce::compute_one(int m, int flag)
input->variable->compute_atom(vidx,igroup,varatom,1,0);
if (flag < 0) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) combine(one,varatom[i],i);
if (mask[i] & groupbit) combine(one,varatom[i],i);
} else one = varatom[flag];
}