forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11455 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
53509fac9f
commit
76e47e855b
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@ -0,0 +1,326 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Pieter in 't Veld (SNL)
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "fix_vector.h"
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#include "update.h"
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#include "force.h"
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#include "modify.h"
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#include "compute.h"
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#include "group.h"
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#include "input.h"
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#include "variable.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum{COMPUTE,FIX,VARIABLE};
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enum{ONE,RUNNING,WINDOW};
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enum{SCALAR,VECTOR};
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#define INVOKED_SCALAR 1
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#define INVOKED_VECTOR 2
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#define INVOKED_ARRAY 4
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/* ---------------------------------------------------------------------- */
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FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 5) error->all(FLERR,"Illegal fix vector command");
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nevery = force->inumeric(FLERR,arg[3]);
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if (nevery <= 0) error->all(FLERR,"Illegal fix vector command");
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nvalues = narg-4;
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which = new int[nvalues];
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argindex = new int[nvalues];
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value2index = new int[nvalues];
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ids = new char*[nvalues];
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nvalues = 0;
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for (int iarg = 4; iarg < narg; iarg++) {
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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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else error->all(FLERR,"Illegal fix vector command");
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int n = strlen(arg[iarg]);
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char *suffix = new char[n];
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strcpy(suffix,&arg[iarg][2]);
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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 vector 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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ids[nvalues] = new char[n];
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strcpy(ids[nvalues],suffix);
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delete [] suffix;
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nvalues++;
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}
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// setup and error check
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// for fix inputs, check that fix frequency is acceptable
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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 vector does not exist");
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if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
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error->all(FLERR,"Fix vector compute does not calculate a scalar");
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if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
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error->all(FLERR,"Fix vector compute does not calculate a vector");
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if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
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error->all(FLERR,
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"Fix vector 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 vector does not exist");
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if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
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error->all(FLERR,"Fix vector fix does not calculate a scalar");
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if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
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error->all(FLERR,"Fix vector fix does not calculate a vector");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
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error->all(FLERR,"Fix vector fix vector is accessed out-of-range");
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if (nevery % modify->fix[ifix]->global_freq)
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error->all(FLERR,
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"Fix for fix vector not computed at compatible time");
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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 vector does not exist");
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if (input->variable->equalstyle(ivariable) == 0)
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error->all(FLERR,"Fix vector variable is not equal-style variable");
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}
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}
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// this fix produces either a global vector or array
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// intensive/extensive flags set by compute,fix,variable that produces value
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global_freq = nevery;
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if (nvalues == 1) {
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vector_flag = 1;
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if (which[0] == COMPUTE) {
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Compute *compute = modify->compute[modify->find_compute(ids[0])];
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if (argindex[0] == 0) extvector = compute->extvector;
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else if (compute->extvector >= 0) extvector = compute->extvector;
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else extvector = compute->extlist[argindex[0]-1];
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} else if (which[0] == FIX) {
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Fix *fix = modify->fix[modify->find_fix(ids[0])];
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if (argindex[0] == 0) extvector = fix->extvector;
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else if (fix->extvector >= 0) extvector = fix->extvector;
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else extvector = fix->extlist[argindex[0]-1];
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} else if (which[0] == VARIABLE)
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extvector = 0;
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} else {
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size_array_cols = nvalues;
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extarray = -1;
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for (int i = 0; i < nvalues; i++) {
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if (which[i] == COMPUTE) {
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Compute *compute = modify->compute[modify->find_compute(ids[i])];
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if (argindex[i] == 0) extlist[i] = compute->extscalar;
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else if (compute->extvector >= 0) extlist[i] = compute->extvector;
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else extlist[i] = compute->extlist[argindex[i]-1];
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} else if (which[i] == FIX) {
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Fix *fix = modify->fix[modify->find_fix(ids[i])];
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if (argindex[i] == 0) extlist[i] = fix->extscalar;
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else if (fix->extvector >= 0) extlist[i] = fix->extvector;
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else extlist[i] = fix->extlist[argindex[i]-1];
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} else if (which[i] == VARIABLE)
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extlist[i] = 0;
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}
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}
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// ncount = current size of vector or array
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vector = NULL;
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array = NULL;
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ncount = 0;
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if (nvalues == 1) size_vector = 0;
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else size_array_rows = 0;
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// nextstep = next step on which end_of_step does something
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// add nextstep to all computes that store invocation times
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// since don't know a priori which are invoked by this fix
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// once in end_of_step() can set timestep for ones actually invoked
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bigint nextstep = (update->ntimestep/nevery)*nevery;
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if (nextstep < update->ntimestep) nextstep += nevery;
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modify->addstep_compute_all(nextstep);
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}
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/* ---------------------------------------------------------------------- */
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FixVector::~FixVector()
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{
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delete [] which;
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delete [] argindex;
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delete [] value2index;
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for (int i = 0; i < nvalues; i++) delete [] ids[i];
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delete [] ids;
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memory->destroy(vector);
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memory->destroy(array);
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}
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/* ---------------------------------------------------------------------- */
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int FixVector::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixVector::init()
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{
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// set current indices for all computes,fixes,variables
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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 vector does not exist");
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value2index[i] = icompute;
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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 vector does not exist");
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value2index[i] = ifix;
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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 vector does not exist");
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value2index[i] = ivariable;
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}
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}
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// reallocate vector or array for size at end of run
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int nsize = (update->laststep-update->firststep+1) / nevery;
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if (nvalues == 1) memory->grow(vector,ncount+nsize,"vector:vector");
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else memory->grow(array,ncount+nsize,nvalues,"vector:array");
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}
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/* ----------------------------------------------------------------------
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only does something if nvalid = current timestep
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------------------------------------------------------------------------- */
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void FixVector::setup(int vflag)
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{
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end_of_step();
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}
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/* ---------------------------------------------------------------------- */
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void FixVector::end_of_step()
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{
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// skip if not step which requires doing something
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if (update->ntimestep % nevery) return;
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// accumulate results of computes,fixes,variables to local copy
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// compute/fix/variable may invoke computes so wrap with clear/add
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double *result;
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if (nvalues == 1) result = &vector[ncount];
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else result = array[ncount];
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modify->clearstep_compute();
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for (int i = 0; i < nvalues; i++) {
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int m = value2index[i];
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// invoke compute if not previously invoked
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if (which[i] == COMPUTE) {
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Compute *compute = modify->compute[m];
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if (argindex[i] == 0) {
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if (!(compute->invoked_flag & INVOKED_SCALAR)) {
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compute->compute_scalar();
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compute->invoked_flag |= INVOKED_SCALAR;
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}
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result[i] = compute->scalar;
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} else {
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if (!(compute->invoked_flag & INVOKED_VECTOR)) {
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compute->compute_vector();
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compute->invoked_flag |= INVOKED_VECTOR;
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}
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result[i] = compute->vector[argindex[i]-1];
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}
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// access fix fields, guaranteed to be ready
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} else if (which[i] == FIX) {
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if (argindex[i] == 0)
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result[i] = modify->fix[m]->compute_scalar();
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else
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result[i] = modify->fix[m]->compute_vector(argindex[i]-1);
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// evaluate equal-style variable
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} else if (which[i] == VARIABLE)
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result[i] = input->variable->compute_equal(m);
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}
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// trigger computes on next needed step
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modify->addstep_compute(update->ntimestep + nevery);
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// update size of vector or array
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ncount++;
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if (nvalues == 1) size_vector++;
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else size_array_rows++;
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}
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/* ----------------------------------------------------------------------
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return Ith vector value
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------------------------------------------------------------------------- */
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double FixVector::compute_vector(int i)
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{
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return vector[i];
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}
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/* ----------------------------------------------------------------------
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return I,J array value
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------------------------------------------------------------------------- */
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double FixVector::compute_array(int i, int j)
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{
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return array[i][j];
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}
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@ -0,0 +1,151 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(vector,FixVector)
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#else
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#ifndef LMP_FIX_VECTOR_H
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#define LMP_FIX_VECTOR_H
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#include "stdio.h"
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixVector : public Fix {
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public:
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FixVector(class LAMMPS *, int, char **);
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~FixVector();
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int setmask();
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void init();
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void setup(int);
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void end_of_step();
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double compute_vector(int);
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double compute_array(int,int);
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private:
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|
int nvalues;
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int *which,*argindex,*value2index,*offcol;
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char **ids;
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int ncount; // # of values currently in growing vector or array
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double *vector;
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double **array;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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|
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|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Compute ID for fix ave/time does not exist
|
||||||
|
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||||||
|
Self-explanatory.
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||||||
|
E: Fix ID for fix ave/time does not exist
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Invalid fix ave/time off column
|
||||||
|
|
||||||
|
Self-explantory.
|
||||||
|
|
||||||
|
E: Fix ave/time compute does not calculate a scalar
|
||||||
|
|
||||||
|
Self-explantory.
|
||||||
|
|
||||||
|
E: Fix ave/time compute does not calculate a vector
|
||||||
|
|
||||||
|
Self-explantory.
|
||||||
|
|
||||||
|
E: Fix ave/time compute vector is accessed out-of-range
|
||||||
|
|
||||||
|
The index for the vector is out of bounds.
|
||||||
|
|
||||||
|
E: Fix ave/time compute does not calculate an array
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time compute array is accessed out-of-range
|
||||||
|
|
||||||
|
An index for the array is out of bounds.
|
||||||
|
|
||||||
|
E: Fix ave/time fix does not calculate a scalar
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time fix does not calculate a vector
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time fix vector is accessed out-of-range
|
||||||
|
|
||||||
|
The index for the vector is out of bounds.
|
||||||
|
|
||||||
|
E: Fix for fix ave/time not computed at compatible time
|
||||||
|
|
||||||
|
Fixes generate their values on specific timesteps. Fix ave/time
|
||||||
|
is requesting a value on a non-allowed timestep.
|
||||||
|
|
||||||
|
E: Fix ave/time fix does not calculate an array
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time fix array is accessed out-of-range
|
||||||
|
|
||||||
|
An index for the array is out of bounds.
|
||||||
|
|
||||||
|
E: Variable name for fix ave/time does not exist
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time variable is not equal-style variable
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time cannot use variable with vector mode
|
||||||
|
|
||||||
|
Variables produce scalar values.
|
||||||
|
|
||||||
|
E: Fix ave/time columns are inconsistent lengths
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Fix ave/time cannot set output array intensive/extensive from these inputs
|
||||||
|
|
||||||
|
One of more of the vector inputs has individual elements which are
|
||||||
|
flagged as intensive or extensive. Such an input cannot be flagged as
|
||||||
|
all intensive/extensive when turned into an array by fix ave/time.
|
||||||
|
|
||||||
|
E: Cannot open fix ave/time file %s
|
||||||
|
|
||||||
|
The specified file cannot be opened. Check that the path and name are
|
||||||
|
correct.
|
||||||
|
|
||||||
|
E: Fix ave/time missed timestep
|
||||||
|
|
||||||
|
You cannot reset the timestep to a value beyond where the fix
|
||||||
|
expects to next perform averaging.
|
||||||
|
|
||||||
|
*/
|
||||||
Loading…
Reference in New Issue