368 lines
13 KiB
C++
368 lines
13 KiB
C++
/* ----------------------------------------------------------------------
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*
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* *** Smooth Mach Dynamics ***
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*
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* This file is part of the USER-SMD package for LAMMPS.
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* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
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* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
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* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
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*
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* ----------------------------------------------------------------------- */
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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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#include "fix_smd_setvel.h"
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#include <mpi.h>
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#include <cstring>
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "domain.h"
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#include "region.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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#include "force.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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enum {
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NONE, CONSTANT, EQUAL, ATOM
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};
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/* ---------------------------------------------------------------------- */
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FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg) {
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if (narg < 6)
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error->all(FLERR, "Illegal fix setvelocity command");
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dynamic_group_allow = 1;
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vector_flag = 1;
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size_vector = 3;
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global_freq = 1;
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extvector = 1;
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xstr = ystr = zstr = NULL;
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if (strstr(arg[3], "v_") == arg[3]) {
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int n = strlen(&arg[3][2]) + 1;
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xstr = new char[n];
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strcpy(xstr, &arg[3][2]);
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} else if (strcmp(arg[3], "NULL") == 0) {
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xstyle = NONE;
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} else {
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xvalue = force->numeric(FLERR, arg[3]);
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xstyle = CONSTANT;
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}
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if (strstr(arg[4], "v_") == arg[4]) {
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int n = strlen(&arg[4][2]) + 1;
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ystr = new char[n];
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strcpy(ystr, &arg[4][2]);
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} else if (strcmp(arg[4], "NULL") == 0) {
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ystyle = NONE;
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} else {
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yvalue = force->numeric(FLERR, arg[4]);
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ystyle = CONSTANT;
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}
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if (strstr(arg[5], "v_") == arg[5]) {
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int n = strlen(&arg[5][2]) + 1;
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zstr = new char[n];
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strcpy(zstr, &arg[5][2]);
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} else if (strcmp(arg[5], "NULL") == 0) {
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zstyle = NONE;
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} else {
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zvalue = force->numeric(FLERR, arg[5]);
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zstyle = CONSTANT;
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}
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// optional args
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iregion = -1;
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idregion = NULL;
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int iarg = 6;
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while (iarg < narg) {
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if (strcmp(arg[iarg], "region") == 0) {
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if (iarg + 2 > narg)
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error->all(FLERR, "Illegal fix setvelocity command");
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iregion = domain->find_region(arg[iarg + 1]);
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if (iregion == -1)
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error->all(FLERR, "Region ID for fix setvelocity does not exist");
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int n = strlen(arg[iarg + 1]) + 1;
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idregion = new char[n];
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strcpy(idregion, arg[iarg + 1]);
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iarg += 2;
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} else
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error->all(FLERR, "Illegal fix setvelocity command");
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}
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force_flag = 0;
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foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
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maxatom = atom->nmax;
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memory->create(sforce, maxatom, 3, "setvelocity:sforce");
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}
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/* ---------------------------------------------------------------------- */
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FixSMDSetVel::~FixSMDSetVel() {
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delete[] xstr;
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delete[] ystr;
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delete[] zstr;
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delete[] idregion;
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memory->destroy(sforce);
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}
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/* ---------------------------------------------------------------------- */
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int FixSMDSetVel::setmask() {
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int mask = 0;
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//mask |= INITIAL_INTEGRATE;
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mask |= POST_FORCE;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixSMDSetVel::init() {
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// check variables
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if (xstr) {
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xvar = input->variable->find(xstr);
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if (xvar < 0)
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error->all(FLERR, "Variable name for fix setvelocity does not exist");
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if (input->variable->equalstyle(xvar))
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xstyle = EQUAL;
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else if (input->variable->atomstyle(xvar))
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xstyle = ATOM;
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else
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error->all(FLERR, "Variable for fix setvelocity is invalid style");
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}
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if (ystr) {
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yvar = input->variable->find(ystr);
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if (yvar < 0)
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error->all(FLERR, "Variable name for fix setvelocity does not exist");
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if (input->variable->equalstyle(yvar))
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ystyle = EQUAL;
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else if (input->variable->atomstyle(yvar))
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ystyle = ATOM;
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else
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error->all(FLERR, "Variable for fix setvelocity is invalid style");
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}
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if (zstr) {
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zvar = input->variable->find(zstr);
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if (zvar < 0)
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error->all(FLERR, "Variable name for fix setvelocity does not exist");
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if (input->variable->equalstyle(zvar))
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zstyle = EQUAL;
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else if (input->variable->atomstyle(zvar))
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zstyle = ATOM;
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else
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error->all(FLERR, "Variable for fix setvelocity is invalid style");
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}
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// set index and check validity of region
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if (iregion >= 0) {
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR, "Region ID for fix setvelocity does not exist");
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}
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if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
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varflag = ATOM;
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else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
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varflag = EQUAL;
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else
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varflag = CONSTANT;
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// cannot use non-zero forces for a minimization since no energy is integrated
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// use fix addforce instead
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int flag = 0;
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if (update->whichflag == 2) {
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if (xstyle == EQUAL || xstyle == ATOM)
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flag = 1;
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if (ystyle == EQUAL || ystyle == ATOM)
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flag = 1;
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if (zstyle == EQUAL || zstyle == ATOM)
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flag = 1;
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if (xstyle == CONSTANT && xvalue != 0.0)
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flag = 1;
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if (ystyle == CONSTANT && yvalue != 0.0)
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flag = 1;
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if (zstyle == CONSTANT && zvalue != 0.0)
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flag = 1;
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}
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if (flag)
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error->all(FLERR, "Cannot use non-zero forces in an energy minimization");
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}
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/* ---------------------------------------------------------------------- */
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void FixSMDSetVel::setup(int vflag) {
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if (strstr(update->integrate_style, "verlet"))
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post_force(vflag);
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else
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error->all(FLERR,"Fix smd/setvel does not support RESPA");
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}
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/* ---------------------------------------------------------------------- */
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void FixSMDSetVel::min_setup(int vflag) {
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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//void FixSMDSetVel::initial_integrate(int vflag) {
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void FixSMDSetVel::post_force(int /*vflag*/) {
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double **x = atom->x;
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double **f = atom->f;
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double **v = atom->v;
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double **vest = atom->vest;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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// update region if necessary
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Region *region = NULL;
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if (iregion >= 0) {
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region = domain->regions[iregion];
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region->prematch();
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}
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// reallocate sforce array if necessary
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if (varflag == ATOM && atom->nmax > maxatom) {
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maxatom = atom->nmax;
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memory->destroy(sforce);
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memory->create(sforce, maxatom, 3, "setvelocity:sforce");
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}
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foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
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force_flag = 0;
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if (varflag == CONSTANT) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2]))
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continue;
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foriginal[0] += f[i][0];
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foriginal[1] += f[i][1];
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foriginal[2] += f[i][2];
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if (xstyle) {
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v[i][0] = xvalue;
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vest[i][0] = xvalue;
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f[i][0] = 0.0;
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}
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if (ystyle) {
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v[i][1] = yvalue;
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vest[i][1] = yvalue;
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f[i][1] = 0.0;
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}
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if (zstyle) {
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v[i][2] = zvalue;
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vest[i][2] = zvalue;
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f[i][2] = 0.0;
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}
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}
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// variable force, wrap with clear/add
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} else {
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modify->clearstep_compute();
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if (xstyle == EQUAL)
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xvalue = input->variable->compute_equal(xvar);
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else if (xstyle == ATOM)
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input->variable->compute_atom(xvar, igroup, &sforce[0][0], 3, 0);
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if (ystyle == EQUAL)
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yvalue = input->variable->compute_equal(yvar);
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else if (ystyle == ATOM)
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input->variable->compute_atom(yvar, igroup, &sforce[0][1], 3, 0);
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if (zstyle == EQUAL)
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zvalue = input->variable->compute_equal(zvar);
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else if (zstyle == ATOM)
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input->variable->compute_atom(zvar, igroup, &sforce[0][2], 3, 0);
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modify->addstep_compute(update->ntimestep + 1);
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//printf("setting velocity at timestep %d\n", update->ntimestep);
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (region && !region->match(x[i][0], x[i][1], x[i][2]))
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continue;
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foriginal[0] += f[i][0];
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foriginal[1] += f[i][1];
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foriginal[2] += f[i][2];
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if (xstyle == ATOM) {
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vest[i][0] = v[i][0] = sforce[i][0];
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f[i][0] = 0.0;
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} else if (xstyle) {
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vest[i][0] = v[i][0] = xvalue;
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f[i][0] = 0.0;
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}
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if (ystyle == ATOM) {
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vest[i][1] = v[i][1] = sforce[i][1];
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f[i][1] = 0.0;
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} else if (ystyle) {
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vest[i][1] = v[i][1] = yvalue;
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f[i][1] = 0.0;
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}
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if (zstyle == ATOM) {
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vest[i][2] = v[i][2] = sforce[i][2];
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f[i][2] = 0.0;
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} else if (zstyle) {
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vest[i][2] = v[i][2] = zvalue;
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f[i][2] = 0.0;
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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return components of total force on fix group before force was changed
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------------------------------------------------------------------------- */
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double FixSMDSetVel::compute_vector(int n) {
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// only sum across procs one time
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if (force_flag == 0) {
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MPI_Allreduce(foriginal, foriginal_all, 3, MPI_DOUBLE, MPI_SUM, world);
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force_flag = 1;
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}
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return foriginal_all[n];
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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double FixSMDSetVel::memory_usage() {
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double bytes = 0.0;
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if (varflag == ATOM)
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bytes = atom->nmax * 3 * sizeof(double);
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return bytes;
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}
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