git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11606 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
302
src/fix_temp_csvr.cpp
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302
src/fix_temp_csvr.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 (ICTP, Italy)
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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_csvr.h"
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#include "atom.h"
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#include "force.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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FixTempCSVR::FixTempCSVR(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/csvr command");
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// CSVR 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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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,"Fix temp/csvr period must be > 0.0");
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if (seed <= 0) error->all(FLERR,"Illegal fix temp/csvr random seed");
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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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random = new RanMars(lmp,seed + comm->me);
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energy = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixTempCSVR::~FixTempCSVR()
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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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}
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/* ---------------------------------------------------------------------- */
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int FixTempCSVR::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 FixTempCSVR::init()
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{
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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/csvr 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/csvr 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/csvr 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 FixTempCSVR::end_of_step()
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{
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double t_current = temperature->compute_scalar();
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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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// set current t_target
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// if variable temp, evaluate variable, wrap with clear/add
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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/csvr variable returned negative temperature");
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modify->addstep_compute(update->ntimestep + nevery);
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}
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// Langevin thermostat, implemented as decribed in
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// Bussi and Parrinello, Phys. Rev. E (2007).
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// it is a linear combination of old velocities and new,
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// randomly chosen, velocity, with proper coefficients
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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const double c1 = exp(-update->dt/t_period);
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if (atom->rmass_flag) { // per atom masses
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const double * const rmass = atom->rmass;
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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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const double m = rmass[i];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*m*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*m*v[i][j]*v[i][j];
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}
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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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const double m = rmass[i];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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temperature->remove_bias(i,v[i]);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*rmass[i]*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*rmass[i]*v[i][j]*v[i][j];
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}
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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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} else { // per atom type masses
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const double * const mass = atom->mass;
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const int * const type = atom->type;
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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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const double m = mass[type[i]];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*m*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*m*v[i][j]*v[i][j];
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}
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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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const double m = mass[type[i]];
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const double c2 = sqrt((1.0-c1*c1)*t_target/m);
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temperature->remove_bias(i,v[i]);
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for (int j = 0; j < 3; ++j) {
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energy += 0.5*m*v[i][j]*v[i][j];
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v[i][j] *= c1;
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v[i][j] += c2*random->gaussian();
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energy -= 0.5*m*v[i][j]*v[i][j];
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}
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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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}
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}
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/* ---------------------------------------------------------------------- */
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int FixTempCSVR::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 FixTempCSVR::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 FixTempCSVR::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 *FixTempCSVR::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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104
src/fix_temp_csvr.h
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104
src/fix_temp_csvr.h
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@ -0,0 +1,104 @@
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/* -*- c++ -*- ----------------------------------------------------------
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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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#ifdef FIX_CLASS
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FixStyle(temp/csvr,FixTempCSVR)
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#else
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#ifndef LMP_FIX_TEMP_CSVR_H
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#define LMP_FIX_TEMP_CSVR_H
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixTempCSVR : public Fix {
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public:
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FixTempCSVR(class LAMMPS *, int, char **);
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~FixTempCSVR();
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int setmask();
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void init();
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void end_of_step();
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int modify_param(int, char **);
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void reset_target(double);
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double compute_scalar();
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virtual void *extract(const char *, int &);
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private:
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int which;
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double t_start,t_stop,t_period,t_target;
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double energy;
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int tstyle,tvar;
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char *tstr;
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char *id_temp;
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class Compute *temperature;
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int tflag;
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class RanMars *random;
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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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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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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.
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E: Fix temp/csvr period must be > 0.0
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Self-explanatory.
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E: Variable name for fix temp/csvr does not exist
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Self-explanatory.
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E: Variable for fix temp/csvr is invalid style
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Only equal-style variables can be used.
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E: Temperature ID for fix temp/csvr does not exist
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Self-explanatory.
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E: Computed temperature for fix temp/csvr cannot be 0.0
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Self-explanatory.
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E: Fix temp/csvr variable returned negative temperature
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Self-explanatory.
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E: Could not find fix_modify temperature ID
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The compute ID for computing temperature does not exist.
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E: Fix_modify temperature ID does not compute temperature
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The compute ID assigned to the fix must compute temperature.
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W: Group for fix_modify temp != fix group
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The fix_modify command is specifying a temperature computation that
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computes a temperature on a different group of atoms than the fix
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itself operates on. This is probably not what you want to do.
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*/
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