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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1272 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-01-02 19:24:46 +00:00
parent 428ca84042
commit b2e9f7dc10
145 changed files with 2801 additions and 2615 deletions
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339
src/fix_ave_atom.cpp
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@ -18,25 +18,99 @@
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{X,V,F,COMPUTE,FIX,VARIABLE};
#define INVOKED_PERATOM 4 // same as in computes
/* ---------------------------------------------------------------------- */
FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all("Illegal fix ave/atom command");
if (narg < 7) error->all("Illegal fix ave/atom command");
nevery = atoi(arg[3]);
nrepeat = atoi(arg[4]);
peratom_freq = atoi(arg[5]);
int n = strlen(arg[6]) + 1;
id_compute = new char[n];
strcpy(id_compute,arg[6]);
// parse remaining values
which = new int[narg-6];
argindex = new int[narg-6];
ids = new char*[narg-6];
value2index = new int[narg-6];
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
ids[nvalues] = NULL;
if (strcmp(arg[iarg],"x") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"y") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"z") == 0) {
which[nvalues] = X;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"vx") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"vy") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"vz") == 0) {
which[nvalues] = V;
argindex[nvalues++] = 2;
} else if (strcmp(arg[iarg],"fx") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 0;
} else if (strcmp(arg[iarg],"fy") == 0) {
which[nvalues] = F;
argindex[nvalues++] = 1;
} else if (strcmp(arg[iarg],"fz") == 0) {
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)) {
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;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all("Illegal fix ave/atom command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else error->all("Illegal fix ave/atom command");
iarg++;
}
// setup and error check
@ -45,24 +119,49 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
(nrepeat-1)*nevery >= peratom_freq)
error->all("Illegal fix ave/atom command");
int icompute = modify->find_compute(id_compute);
if (icompute < 0) error->all("Compute ID for fix ave/atom does not exist");
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/atom does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/atom compute does not calculate per-atom values");
if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
error->all("Fix ave/atom compute does not calculate a per-atom scalar");
if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
error->all("Fix ave/atom compute does not calculate a per-atom vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom)
error->all("Fix ave/atom 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/atom does not exist");
if (modify->fix[ifix]->peratom_flag == 0)
error->all("Fix ave/atom fix does not calculate per-atom values");
if (argindex[i] && modify->fix[ifix]->size_peratom != 0)
error->all("Fix ave/atom fix does not calculate a per-atom scalar");
if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
error->all("Fix ave/atom fix does not calculate a per-atom vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom)
error->all("Fix ave/atom 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/atom does not exist");
if (input->variable->atomstyle(ivariable) == 0)
error->all("Fix ave/atom variable is not atom-style variable");
}
}
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/atom compute does not calculate per-atom info");
// this fix produces either a per-atom scalar or vector
peratom_flag = 1;
// setup list of computes to call, including pre-computes
ncompute = 1 + modify->compute[icompute]->npre;
compute = new Compute*[ncompute];
if (nvalues == 1) size_peratom = 0;
else size_peratom = nvalues;
// perform initial allocation of atom-based array
// register with Atom class
size_peratom = modify->compute[icompute]->size_peratom;
scalar = NULL;
vector = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
@ -70,13 +169,10 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
// zero the array since dump may access it on timestep 0
int nlocal = atom->nlocal;
if (size_peratom == 0)
for (int i = 0; i < nlocal; i++) scalar[i] = 0.0;
else
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < size_peratom; m++)
vector[i][m] = 0.0;
for (int i = 0; i < nlocal; i++)
for (int m = 0; m < nvalues; m++)
vector[i][m] = 0.0;
// nvalid = next step on which end_of_step does something
// can be this timestep if multiple of peratom_freq and nrepeat = 1
// else backup from next multiple of peratom_freq
@ -89,12 +185,11 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += peratom_freq;
// set timestep for all computes that store invocation times
// since don't know a priori which are invoked by this fix
// add nvalid to ALL computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can just set timestep for ones actually invoked
for (int i = 0; i < modify->ncompute; i++)
if (modify->compute[i]->timeflag) modify->compute[i]->add_step(nvalid);
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
@ -105,9 +200,12 @@ FixAveAtom::~FixAveAtom()
atom->delete_callback(id,0);
delete [] id_compute;
delete [] compute;
memory->sfree(scalar);
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->destroy_2d_double_array(vector);
}
@ -124,29 +222,49 @@ int FixAveAtom::setmask()
void FixAveAtom::init()
{
// set ptrs to compute and its pre-computes called each end-of-step
// put pre-computes in list before compute
// set indices and check validity of all computes,fixes,variables
// check that fix frequency is acceptable
int icompute = modify->find_compute(id_compute);
if (icompute < 0) error->all("Compute ID for fix ave/atom does not exist");
ncompute = 0;
if (modify->compute[icompute]->npre)
for (int i = 0; i < modify->compute[icompute]->npre; i++) {
int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
if (ic < 0)
error->all("Precompute ID of compute for fix ave/atom does not exist");
compute[ncompute++] = modify->compute[ic];
}
for (int m = 0; m < nvalues; m++) {
if (which[m] == COMPUTE) {
int icompute = modify->find_compute(ids[m]);
if (icompute < 0)
error->all("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("Fix ID for fix ave/atom does not exist");
value2index[m] = ifix;
compute[ncompute++] = modify->compute[icompute];
if (nevery % modify->fix[ifix]->peratom_freq)
error->all("Fix for fix ave/atom 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/atom does not exist");
value2index[m] = ivariable;
} else value2index[m] = -1;
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveAtom::setup()
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveAtom::end_of_step()
{
int i,m;
int i,j,m,n;
// skip if not step which requires doing something
@ -156,32 +274,70 @@ void FixAveAtom::end_of_step()
int nlocal = atom->nlocal;
if (irepeat == 0) {
if (size_peratom == 0)
for (i = 0; i < nlocal; i++) scalar[i] = 0.0;
else
for (i = 0; i < nlocal; i++)
for (m = 0; m < size_peratom; m++)
vector[i][m] = 0.0;
}
// accumulate results of compute to local copy
if (irepeat == 0)
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
vector[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
modify->clearstep_compute();
for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
int *mask = atom->mask;
if (size_peratom == 0) {
double *compute_scalar = compute[ncompute-1]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) scalar[i] += compute_scalar[i];
} else {
double **compute_vector = compute[ncompute-1]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
for (m = 0; m < size_peratom; m++)
vector[i][m] += compute_vector[i][m];
for (m = 0; m < nvalues; m++) {
n = value2index[m];
j = argindex[m];
if (which[m] == X) {
double **x = atom->x;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += x[i][j];
} else if (which[m] == V) {
double **v = atom->v;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += v[i][j];
} else if (which[m] == F) {
double **f = atom->f;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += f[i][j];
// invoke compute if not previously invoked
} else if (which[m] == COMPUTE) {
Compute *compute = modify->compute[n];
if (!(compute->invoked & INVOKED_PERATOM)) compute->compute_peratom();
if (j == 0) {
double *compute_scalar = compute->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += compute_scalar[i];
} else {
int jm1 = j - 1;
double **compute_vector = compute->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += compute_vector[i][jm1];
}
// access fix fields, guaranteed to be ready
} else if (which[m] == FIX) {
if (j == 0) {
double *fix_scalar = modify->fix[n]->scalar_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += fix_scalar[i];
} else {
int jm1 = j - 1;
double **fix_vector = modify->fix[n]->vector_atom;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) vector[i][m] += fix_vector[i][jm1];
}
// evaluate atom-style variable
} else if (which[m] == VARIABLE)
input->variable->compute_atom(n,igroup,&vector[0][m],nvalues,1);
}
// done if irepeat < nrepeat
@ -201,13 +357,9 @@ void FixAveAtom::end_of_step()
// average the final result for the Nfreq timestep
double repeat = nrepeat;
if (size_peratom == 0)
for (i = 0; i < nlocal; i++)
scalar[i] /= repeat;
else
for (i = 0; i < nlocal; i++)
for (m = 0; m < size_peratom; m++)
vector[i][m] /= repeat;
for (i = 0; i < nlocal; i++)
for (m = 0; m < nvalues; m++)
vector[i][m] /= repeat;
}
/* ----------------------------------------------------------------------
@ -217,8 +369,7 @@ void FixAveAtom::end_of_step()
double FixAveAtom::memory_usage()
{
double bytes;
if (size_peratom == 0) bytes = atom->nmax * sizeof(double);
else bytes = atom->nmax*size_peratom * sizeof(double);
bytes = atom->nmax*nvalues * sizeof(double);
return bytes;
}
@ -228,15 +379,10 @@ double FixAveAtom::memory_usage()
void FixAveAtom::grow_arrays(int nmax)
{
if (size_peratom == 0) {
scalar = (double *) memory->srealloc(scalar,nmax*sizeof(double),
"fix_ave/atom:scalar");
scalar_atom = scalar;
} else {
vector = memory->grow_2d_double_array(vector,nmax,size_peratom,
"fix_ave/atom:vector");
vector_atom = vector;
}
vector = memory->grow_2d_double_array(vector,nmax,nvalues,
"fix_ave/atom:vector");
vector_atom = vector;
scalar_atom = vector[0];
}
/* ----------------------------------------------------------------------
@ -245,11 +391,8 @@ void FixAveAtom::grow_arrays(int nmax)
void FixAveAtom::copy_arrays(int i, int j)
{
if (size_peratom == 0)
scalar[j] = scalar[i];
else
for (int m = 0; m <= size_peratom; m++)
vector[j][m] = vector[i][m];
for (int m = 0; m < nvalues; m++)
vector[j][m] = vector[i][m];
}
/* ----------------------------------------------------------------------
@ -258,13 +401,8 @@ void FixAveAtom::copy_arrays(int i, int j)
int FixAveAtom::pack_exchange(int i, double *buf)
{
if (size_peratom == 0) {
buf[0] = scalar[i];
return 1;
}
for (int m = 0; m <= size_peratom; m++) buf[m] = vector[i][m];
return size_peratom;
for (int m = 0; m < nvalues; m++) buf[m] = vector[i][m];
return nvalues;
}
/* ----------------------------------------------------------------------
@ -273,11 +411,6 @@ int FixAveAtom::pack_exchange(int i, double *buf)
int FixAveAtom::unpack_exchange(int nlocal, double *buf)
{
if (size_peratom == 0) {
scalar[nlocal] = buf[0];
return 1;
}
for (int m = 0; m <= size_peratom; m++) vector[nlocal][m] = buf[m];
return size_peratom;
for (int m = 0; m < nvalues; m++) vector[nlocal][m] = buf[m];
return nvalues;
}