git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13320 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/fix_temp_csld.cpp
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307
src/fix_temp_csld.cpp
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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: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "string.h"
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#include "stdlib.h"
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#include "math.h"
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#include "fix_temp_csld.h"
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#include "atom.h"
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#include "force.h"
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#include "memory.h"
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#include "comm.h"
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#include "input.h"
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#include "variable.h"
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#include "group.h"
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#include "update.h"
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#include "modify.h"
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#include "compute.h"
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#include "random_mars.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{NOBIAS,BIAS};
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enum{CONSTANT,EQUAL};
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/* ---------------------------------------------------------------------- */
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FixTempCSLD::FixTempCSLD(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 7) error->all(FLERR,"Illegal fix temp/csld command");
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// CSLD thermostat should be applied every step
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nevery = 1;
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scalar_flag = 1;
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global_freq = nevery;
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dynamic_group_allow = 1;
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extscalar = 1;
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tstr = 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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tstr = new char[n];
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strcpy(tstr,&arg[3][2]);
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tstyle = EQUAL;
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} else {
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t_start = force->numeric(FLERR,arg[3]);
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t_target = t_start;
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tstyle = CONSTANT;
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}
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t_stop = force->numeric(FLERR,arg[4]);
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t_period = force->numeric(FLERR,arg[5]);
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int seed = force->inumeric(FLERR,arg[6]);
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// error checks
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if (t_period <= 0.0) error->all(FLERR,"Illegal fix temp/csld command");
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if (seed <= 0) error->all(FLERR,"Illegal fix temp/csld command");
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random = new RanMars(lmp,seed + comm->me);
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// create a new compute temp style
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// id = fix-ID + temp, compute group = fix group
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int n = strlen(id) + 6;
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id_temp = new char[n];
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strcpy(id_temp,id);
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strcat(id_temp,"_temp");
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char **newarg = new char*[3];
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newarg[0] = id_temp;
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newarg[1] = group->names[igroup];
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newarg[2] = (char *) "temp";
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modify->add_compute(3,newarg);
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delete [] newarg;
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tflag = 1;
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vhold = NULL;
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nmax = -1;
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energy = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixTempCSLD::~FixTempCSLD()
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{
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delete [] tstr;
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// delete temperature if fix created it
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if (tflag) modify->delete_compute(id_temp);
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delete [] id_temp;
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delete random;
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memory->destroy(vhold);
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vhold = NULL;
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nmax = -1;
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}
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/* ---------------------------------------------------------------------- */
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int FixTempCSLD::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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mask |= THERMO_ENERGY;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixTempCSLD::init()
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{
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// we cannot handle constraints via rattle or shake correctly.
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int has_shake = 0;
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for (int i = 0; i < modify->nfix; i++)
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if ((strcmp(modify->fix[i]->style,"shake") == 0)
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|| (strcmp(modify->fix[i]->style,"rattle") == 0)) ++has_shake;
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if (has_shake > 0)
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error->all(FLERR,"Fix temp/csld is not compatible with fix rattle or fix shake");
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// check variable
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if (tstr) {
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tvar = input->variable->find(tstr);
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if (tvar < 0)
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error->all(FLERR,"Variable name for fix temp/csld does not exist");
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if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
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else error->all(FLERR,"Variable for fix temp/csld is invalid style");
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}
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0)
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error->all(FLERR,"Temperature ID for fix temp/csld does not exist");
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temperature = modify->compute[icompute];
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if (temperature->tempbias) which = BIAS;
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else which = NOBIAS;
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}
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/* ---------------------------------------------------------------------- */
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void FixTempCSLD::end_of_step()
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{
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// set current t_target
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// if variable temp, evaluate variable, wrap with clear/add
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double delta = update->ntimestep - update->beginstep;
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if (delta != 0.0) delta /= update->endstep - update->beginstep;
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if (tstyle == CONSTANT)
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t_target = t_start + delta * (t_stop-t_start);
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else {
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modify->clearstep_compute();
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t_target = input->variable->compute_equal(tvar);
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if (t_target < 0.0)
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error->one(FLERR,
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"Fix temp/csld variable returned negative temperature");
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modify->addstep_compute(update->ntimestep + nevery);
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}
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double t_current = temperature->compute_scalar();
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double ekin_old = t_current * 0.5 * temperature->dof * force->boltz;
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double * const * const v = atom->v;
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const int * const mask = atom->mask;
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const int * const type = atom->type;
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const int nlocal = atom->nlocal;
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// adjust holding space, if needed and copy existing velocities
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if (nmax < atom->nlocal) {
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nmax = atom->nlocal + 1;
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memory->destroy(vhold);
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memory->create(vhold,nmax,3,"csld:vhold");
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}
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// The CSLD thermostat is a linear combination of old and new velocities,
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// where the new ones are randomly chosen from a gaussian distribution.
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// see Bussi and Parrinello, Phys. Rev. E (2007).
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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double m;
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if (atom->rmass_flag) m = atom->rmass[i];
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else m = atom->mass[type[i]];
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const double factor = 1.0/sqrt(m);
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const double vx = random->gaussian() * factor;
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vhold[i][0] = v[i][0];
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v[i][0] = vx;
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const double vy = random->gaussian() * factor;
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vhold[i][1] = v[i][1];
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v[i][1] = vy;
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const double vz = random->gaussian() * factor;
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vhold[i][2] = v[i][2];
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v[i][2] = vz;
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}
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}
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// mixing factors
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const double c1 = exp(-update->dt/t_period);
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const double c2 = sqrt((1.0-c1*c1)*t_target/temperature->compute_scalar());
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if (which == NOBIAS) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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v[i][0] = vhold[i][0]*c1 + v[i][0]*c2;
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v[i][1] = vhold[i][1]*c1 + v[i][1]*c2;
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v[i][2] = vhold[i][2]*c1 + v[i][2]*c2;
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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temperature->remove_bias(i,vhold[i]);
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v[i][0] = vhold[i][0]*c1 + v[i][0]*c2;
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v[i][1] = vhold[i][1]*c1 + v[i][1]*c2;
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v[i][2] = vhold[i][2]*c1 + v[i][2]*c2;
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temperature->restore_bias(i,v[i]);
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}
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}
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}
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// tally the kinetic energy transferred between heat bath and system
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t_current = temperature->compute_scalar();
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energy += ekin_old - t_current * 0.5 * temperature->dof * force->boltz;
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}
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/* ---------------------------------------------------------------------- */
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int FixTempCSLD::modify_param(int narg, char **arg)
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{
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if (strcmp(arg[0],"temp") == 0) {
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if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
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if (tflag) {
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modify->delete_compute(id_temp);
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tflag = 0;
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}
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delete [] id_temp;
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int n = strlen(arg[1]) + 1;
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id_temp = new char[n];
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strcpy(id_temp,arg[1]);
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int icompute = modify->find_compute(id_temp);
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if (icompute < 0)
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error->all(FLERR,"Could not find fix_modify temperature ID");
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temperature = modify->compute[icompute];
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if (temperature->tempflag == 0)
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error->all(FLERR,
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"Fix_modify temperature ID does not compute temperature");
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if (temperature->igroup != igroup && comm->me == 0)
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error->warning(FLERR,"Group for fix_modify temp != fix group");
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return 2;
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}
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return 0;
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}
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/* ---------------------------------------------------------------------- */
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void FixTempCSLD::reset_target(double t_new)
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{
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t_target = t_start = t_stop = t_new;
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}
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/* ---------------------------------------------------------------------- */
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double FixTempCSLD::compute_scalar()
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{
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return energy;
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}
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/* ----------------------------------------------------------------------
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extract thermostat properties
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------------------------------------------------------------------------- */
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void *FixTempCSLD::extract(const char *str, int &dim)
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{
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dim=0;
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if (strcmp(str,"t_target") == 0) {
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return &t_target;
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}
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return NULL;
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}
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