git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5717 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
592
src/update.cpp
592
src/update.cpp
@ -1,296 +1,296 @@
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/* ----------------------------------------------------------------------
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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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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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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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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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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certain rights in this software. This software is distributed under
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the GNU General Public License.
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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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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "string.h"
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#include "stdlib.h"
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#include "stdlib.h"
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#include "update.h"
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#include "update.h"
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#include "style_integrate.h"
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#include "style_integrate.h"
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#include "style_minimize.h"
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#include "style_minimize.h"
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#include "neighbor.h"
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#include "neighbor.h"
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#include "force.h"
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#include "force.h"
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#include "modify.h"
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#include "modify.h"
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#include "fix.h"
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#include "fix.h"
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#include "domain.h"
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#include "domain.h"
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#include "region.h"
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#include "region.h"
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#include "compute.h"
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#include "compute.h"
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#include "output.h"
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#include "output.h"
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#include "memory.h"
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#include "memory.h"
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#include "error.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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Update::Update(LAMMPS *lmp) : Pointers(lmp)
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Update::Update(LAMMPS *lmp) : Pointers(lmp)
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{
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{
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int n;
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int n;
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char *str;
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char *str;
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ntimestep = 0;
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ntimestep = 0;
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first_update = 0;
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first_update = 0;
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whichflag = 0;
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whichflag = 0;
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firststep = laststep = 0;
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firststep = laststep = 0;
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beginstep = endstep = 0;
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beginstep = endstep = 0;
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setupflag = 0;
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setupflag = 0;
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multireplica = 0;
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multireplica = 0;
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restrict_output = 0;
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restrict_output = 0;
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eflag_global = vflag_global = -1;
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eflag_global = vflag_global = -1;
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unit_style = NULL;
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unit_style = NULL;
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set_units("lj");
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set_units("lj");
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str = (char *) "verlet";
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str = (char *) "verlet";
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n = strlen(str) + 1;
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n = strlen(str) + 1;
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integrate_style = new char[n];
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integrate_style = new char[n];
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strcpy(integrate_style,str);
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strcpy(integrate_style,str);
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integrate = new Verlet(lmp,0,NULL);
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integrate = new Verlet(lmp,0,NULL);
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str = (char *) "cg";
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str = (char *) "cg";
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n = strlen(str) + 1;
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n = strlen(str) + 1;
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minimize_style = new char[n];
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minimize_style = new char[n];
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strcpy(minimize_style,str);
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strcpy(minimize_style,str);
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minimize = new MinCG(lmp);
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minimize = new MinCG(lmp);
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}
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}
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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Update::~Update()
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Update::~Update()
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{
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{
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delete [] unit_style;
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delete [] unit_style;
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delete [] integrate_style;
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delete [] integrate_style;
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delete integrate;
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delete integrate;
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delete [] minimize_style;
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delete [] minimize_style;
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delete minimize;
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delete minimize;
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}
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}
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void Update::init()
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void Update::init()
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{
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{
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// init the appropriate integrate and/or minimize class
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// init the appropriate integrate and/or minimize class
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// if neither (e.g. from write_restart) then just return
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// if neither (e.g. from write_restart) then just return
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if (whichflag == 0) return;
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if (whichflag == 0) return;
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if (whichflag == 1) integrate->init();
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if (whichflag == 1) integrate->init();
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else if (whichflag == 2) minimize->init();
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else if (whichflag == 2) minimize->init();
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// only set first_update if a run or minimize is being performed
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// only set first_update if a run or minimize is being performed
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first_update = 1;
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first_update = 1;
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}
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}
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void Update::set_units(const char *style)
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void Update::set_units(const char *style)
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{
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{
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// physical constants from:
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// physical constants from:
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// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
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// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
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// using thermochemical calorie = 4.184 J
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// using thermochemical calorie = 4.184 J
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if (strcmp(style,"lj") == 0) {
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if (strcmp(style,"lj") == 0) {
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force->boltz = 1.0;
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force->boltz = 1.0;
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force->mvv2e = 1.0;
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force->mvv2e = 1.0;
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force->ftm2v = 1.0;
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force->ftm2v = 1.0;
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force->mv2d = 1.0;
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force->mv2d = 1.0;
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force->nktv2p = 1.0;
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force->nktv2p = 1.0;
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force->qqr2e = 1.0;
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force->qqr2e = 1.0;
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force->qe2f = 1.0;
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force->qe2f = 1.0;
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force->vxmu2f = 1.0;
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force->vxmu2f = 1.0;
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force->xxt2kmu = 1.0;
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force->xxt2kmu = 1.0;
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dt = 0.005;
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dt = 0.005;
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neighbor->skin = 0.3;
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neighbor->skin = 0.3;
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} else if (strcmp(style,"real") == 0) {
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} else if (strcmp(style,"real") == 0) {
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force->boltz = 0.0019872067;
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force->boltz = 0.0019872067;
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force->mvv2e = 48.88821291 * 48.88821291;
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force->mvv2e = 48.88821291 * 48.88821291;
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force->ftm2v = 1.0 / 48.88821291 / 48.88821291;
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force->ftm2v = 1.0 / 48.88821291 / 48.88821291;
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force->mv2d = 1.0 / 0.602214179;
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force->mv2d = 1.0 / 0.602214179;
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force->nktv2p = 68568.415;
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force->nktv2p = 68568.415;
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force->qqr2e = 332.06371;
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force->qqr2e = 332.06371;
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force->qe2f = 23.060549;
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force->qe2f = 23.060549;
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force->vxmu2f = 1.4393264316e4;
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force->vxmu2f = 1.4393264316e4;
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force->xxt2kmu = 0.1;
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force->xxt2kmu = 0.1;
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dt = 1.0;
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dt = 1.0;
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neighbor->skin = 2.0;
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neighbor->skin = 2.0;
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} else if (strcmp(style,"metal") == 0) {
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} else if (strcmp(style,"metal") == 0) {
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force->boltz = 8.617343e-5;
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force->boltz = 8.617343e-5;
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force->mvv2e = 1.0364269e-4;
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force->mvv2e = 1.0364269e-4;
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force->ftm2v = 1.0 / 1.0364269e-4;
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force->ftm2v = 1.0 / 1.0364269e-4;
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force->mv2d = 1.0 / 0.602214179;
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force->mv2d = 1.0 / 0.602214179;
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force->nktv2p = 1.6021765e6;
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force->nktv2p = 1.6021765e6;
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force->qqr2e = 14.399645;
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force->qqr2e = 14.399645;
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force->qe2f = 1.0;
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force->qe2f = 1.0;
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force->vxmu2f = 0.6241509647;
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force->vxmu2f = 0.6241509647;
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force->xxt2kmu = 1.0e-4;
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force->xxt2kmu = 1.0e-4;
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dt = 0.001;
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dt = 0.001;
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neighbor->skin = 2.0;
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neighbor->skin = 2.0;
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} else if (strcmp(style,"si") == 0) {
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} else if (strcmp(style,"si") == 0) {
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force->boltz = 1.3806504e-23;
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force->boltz = 1.3806504e-23;
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force->mvv2e = 1.0;
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force->mvv2e = 1.0;
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force->ftm2v = 1.0;
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force->ftm2v = 1.0;
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force->mv2d = 1.0;
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force->mv2d = 1.0;
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force->nktv2p = 1.0;
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force->nktv2p = 1.0;
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force->qqr2e = 8.9876e9;
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force->qqr2e = 8.9876e9;
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force->qe2f = 1.0;
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force->qe2f = 1.0;
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force->vxmu2f = 1.0;
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force->vxmu2f = 1.0;
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force->xxt2kmu = 1.0;
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force->xxt2kmu = 1.0;
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dt = 1.0e-8;
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dt = 1.0e-8;
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neighbor->skin = 0.001;
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neighbor->skin = 0.001;
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} else if (strcmp(style,"cgs") == 0) {
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} else if (strcmp(style,"cgs") == 0) {
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force->boltz = 1.3806504e-16;
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force->boltz = 1.3806504e-16;
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force->mvv2e = 1.0;
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force->mvv2e = 1.0;
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force->ftm2v = 1.0;
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force->ftm2v = 1.0;
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force->mv2d = 1.0;
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force->mv2d = 1.0;
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force->nktv2p = 1.0;
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force->nktv2p = 1.0;
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force->qqr2e = 1.0;
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force->qqr2e = 1.0;
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force->qe2f = 1.0;
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force->qe2f = 1.0;
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force->vxmu2f = 1.0;
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force->vxmu2f = 1.0;
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force->xxt2kmu = 1.0;
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force->xxt2kmu = 1.0;
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dt = 1.0e-8;
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dt = 1.0e-8;
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neighbor->skin = 0.1;
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neighbor->skin = 0.1;
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} else if (strcmp(style,"electron") == 0) {
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} else if (strcmp(style,"electron") == 0) {
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force->boltz = 3.16679e-6;
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force->boltz = 3.16681534e-6;
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force->mvv2e = 1.0;
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force->mvv2e = 1.06657236;
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force->ftm2v = 1 / 1.0327499;
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force->ftm2v = 0.937582899;
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force->mv2d = 1.0;
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force->mv2d = 1.0;
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force->nktv2p = 2.9421e13;
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force->nktv2p = 2.94210108e13;
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force->qqr2e = 1.0;
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force->qqr2e = 1.0;
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force->qe2f = 1.0;
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force->qe2f = 1.94469051e-10;
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force->vxmu2f = 0.6241509647;
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force->vxmu2f = 3.39893149e1;
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force->xxt2kmu = 1.0e-4;
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force->xxt2kmu = 3.13796367e-2;
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dt = 0.001;
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dt = 0.001;
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neighbor->skin = 2.0;
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neighbor->skin = 2.0;
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} else error->all("Illegal units command");
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} else error->all("Illegal units command");
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delete [] unit_style;
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delete [] unit_style;
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int n = strlen(style) + 1;
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int n = strlen(style) + 1;
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unit_style = new char[n];
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unit_style = new char[n];
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strcpy(unit_style,style);
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strcpy(unit_style,style);
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}
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}
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/* ---------------------------------------------------------------------- */
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/* ---------------------------------------------------------------------- */
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void Update::create_integrate(int narg, char **arg)
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void Update::create_integrate(int narg, char **arg)
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{
|
{
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if (narg < 1) error->all("Illegal run_style command");
|
if (narg < 1) error->all("Illegal run_style command");
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|
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delete [] integrate_style;
|
delete [] integrate_style;
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delete integrate;
|
delete integrate;
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|
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if (0) return; // dummy line to enable else-if macro expansion
|
if (0) return; // dummy line to enable else-if macro expansion
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|
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#define INTEGRATE_CLASS
|
#define INTEGRATE_CLASS
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#define IntegrateStyle(key,Class) \
|
#define IntegrateStyle(key,Class) \
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else if (strcmp(arg[0],#key) == 0) integrate = new Class(lmp,narg-1,&arg[1]);
|
else if (strcmp(arg[0],#key) == 0) integrate = new Class(lmp,narg-1,&arg[1]);
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#include "style_integrate.h"
|
#include "style_integrate.h"
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#undef INTEGRATE_CLASS
|
#undef INTEGRATE_CLASS
|
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|
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else error->all("Illegal run_style command");
|
else error->all("Illegal run_style command");
|
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|
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int n = strlen(arg[0]) + 1;
|
int n = strlen(arg[0]) + 1;
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integrate_style = new char[n];
|
integrate_style = new char[n];
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strcpy(integrate_style,arg[0]);
|
strcpy(integrate_style,arg[0]);
|
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}
|
}
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|
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/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
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void Update::create_minimize(int narg, char **arg)
|
void Update::create_minimize(int narg, char **arg)
|
||||||
{
|
{
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if (narg != 1) error->all("Illegal min_style command");
|
if (narg != 1) error->all("Illegal min_style command");
|
||||||
|
|
||||||
delete [] minimize_style;
|
delete [] minimize_style;
|
||||||
delete minimize;
|
delete minimize;
|
||||||
|
|
||||||
if (0) return; // dummy line to enable else-if macro expansion
|
if (0) return; // dummy line to enable else-if macro expansion
|
||||||
|
|
||||||
#define MINIMIZE_CLASS
|
#define MINIMIZE_CLASS
|
||||||
#define MinimizeStyle(key,Class) \
|
#define MinimizeStyle(key,Class) \
|
||||||
else if (strcmp(arg[0],#key) == 0) minimize = new Class(lmp);
|
else if (strcmp(arg[0],#key) == 0) minimize = new Class(lmp);
|
||||||
#include "style_minimize.h"
|
#include "style_minimize.h"
|
||||||
#undef MINIMIZE_CLASS
|
#undef MINIMIZE_CLASS
|
||||||
|
|
||||||
else error->all("Illegal min_style command");
|
else error->all("Illegal min_style command");
|
||||||
|
|
||||||
int n = strlen(arg[0]) + 1;
|
int n = strlen(arg[0]) + 1;
|
||||||
minimize_style = new char[n];
|
minimize_style = new char[n];
|
||||||
strcpy(minimize_style,arg[0]);
|
strcpy(minimize_style,arg[0]);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
reset timestep from input script
|
reset timestep from input script
|
||||||
do not allow dump files or a restart to be defined
|
do not allow dump files or a restart to be defined
|
||||||
do not allow any timestep-dependent fixes to be defined
|
do not allow any timestep-dependent fixes to be defined
|
||||||
do not allow any dynamic regions to be defined
|
do not allow any dynamic regions to be defined
|
||||||
reset eflag/vflag global so nothing will think eng/virial are current
|
reset eflag/vflag global so nothing will think eng/virial are current
|
||||||
reset invoked flags of computes,
|
reset invoked flags of computes,
|
||||||
so nothing will think they are current between runs
|
so nothing will think they are current between runs
|
||||||
clear timestep list of computes that store future invocation times
|
clear timestep list of computes that store future invocation times
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void Update::reset_timestep(int narg, char **arg)
|
void Update::reset_timestep(int narg, char **arg)
|
||||||
{
|
{
|
||||||
if (narg != 1) error->all("Illegal reset_timestep command");
|
if (narg != 1) error->all("Illegal reset_timestep command");
|
||||||
|
|
||||||
for (int i = 0; i < output->ndump; i++)
|
for (int i = 0; i < output->ndump; i++)
|
||||||
if (output->last_dump[i] >= 0)
|
if (output->last_dump[i] >= 0)
|
||||||
error->all("Cannot reset timestep with dump file already written to");
|
error->all("Cannot reset timestep with dump file already written to");
|
||||||
if (output->restart && output->last_restart >= 0)
|
if (output->restart && output->last_restart >= 0)
|
||||||
error->all("Cannot reset timestep with restart file already written");
|
error->all("Cannot reset timestep with restart file already written");
|
||||||
|
|
||||||
for (int i = 0; i < modify->nfix; i++)
|
for (int i = 0; i < modify->nfix; i++)
|
||||||
if (modify->fix[i]->time_depend)
|
if (modify->fix[i]->time_depend)
|
||||||
error->all("Cannot reset timestep with a time-dependent fix defined");
|
error->all("Cannot reset timestep with a time-dependent fix defined");
|
||||||
|
|
||||||
for (int i = 0; i < domain->nregion; i++)
|
for (int i = 0; i < domain->nregion; i++)
|
||||||
if (domain->regions[i]->dynamic_check())
|
if (domain->regions[i]->dynamic_check())
|
||||||
error->all("Cannot reset timestep with a dynamic region defined");
|
error->all("Cannot reset timestep with a dynamic region defined");
|
||||||
|
|
||||||
eflag_global = vflag_global = -1;
|
eflag_global = vflag_global = -1;
|
||||||
|
|
||||||
for (int i = 0; i < modify->ncompute; i++) {
|
for (int i = 0; i < modify->ncompute; i++) {
|
||||||
modify->compute[i]->invoked_scalar = -1;
|
modify->compute[i]->invoked_scalar = -1;
|
||||||
modify->compute[i]->invoked_vector = -1;
|
modify->compute[i]->invoked_vector = -1;
|
||||||
modify->compute[i]->invoked_array = -1;
|
modify->compute[i]->invoked_array = -1;
|
||||||
modify->compute[i]->invoked_peratom = -1;
|
modify->compute[i]->invoked_peratom = -1;
|
||||||
modify->compute[i]->invoked_local = -1;
|
modify->compute[i]->invoked_local = -1;
|
||||||
}
|
}
|
||||||
|
|
||||||
for (int i = 0; i < modify->ncompute; i++)
|
for (int i = 0; i < modify->ncompute; i++)
|
||||||
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
|
if (modify->compute[i]->timeflag) modify->compute[i]->clearstep();
|
||||||
|
|
||||||
ntimestep = ATOBIGINT(arg[0]);
|
ntimestep = ATOBIGINT(arg[0]);
|
||||||
if (ntimestep < 0) error->all("Timestep must be >= 0");
|
if (ntimestep < 0) error->all("Timestep must be >= 0");
|
||||||
if (ntimestep > MAXBIGINT) error->all("Too big a timestep");
|
if (ntimestep > MAXBIGINT) error->all("Too big a timestep");
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
memory usage of update and integrate/minimize
|
memory usage of update and integrate/minimize
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
double Update::memory_usage()
|
double Update::memory_usage()
|
||||||
{
|
{
|
||||||
double bytes = 0.0;
|
double bytes = 0.0;
|
||||||
if (whichflag == 1) bytes += integrate->memory_usage();
|
if (whichflag == 1) bytes += integrate->memory_usage();
|
||||||
else if (whichflag == 2) bytes += minimize->memory_usage();
|
else if (whichflag == 2) bytes += minimize->memory_usage();
|
||||||
return bytes;
|
return bytes;
|
||||||
}
|
}
|
||||||
|
|||||||
Reference in New Issue
Block a user