diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp index 3ef99ccd8..ae5868ff0 100644 --- a/src/fix_temp_csvr.cpp +++ b/src/fix_temp_csvr.cpp @@ -1,344 +1,349 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing author: Axel Kohlmeyer (Temple U) Based on code by Paolo Raiteri (Curtin U) and Giovanni Bussi (SISSA) ------------------------------------------------------------------------- */ #include #include #include #include "fix_temp_csvr.h" #include "atom.h" #include "force.h" #include "memory.h" #include "comm.h" #include "input.h" #include "variable.h" #include "group.h" #include "update.h" #include "modify.h" #include "compute.h" #include "random_mars.h" #include "error.h" using namespace LAMMPS_NS; using namespace FixConst; enum{NOBIAS,BIAS}; enum{CONSTANT,EQUAL}; double FixTempCSVR::gamdev(const int ia) { int j; double am,e,s,v1,v2,x,y; if (ia < 1) return 0.0; if (ia < 6) { x=1.0; for (j=1; j<=ia; j++) x *= random->uniform(); - x = -log(x); + + // make certain, that -log() doesn't overflow. + if (x < 2.2250759805e-308) + x = 708.4; + else + x = -log(x); } else { restart: do { do { do { v1 = random->uniform(); v2 = 2.0*random->uniform() - 1.0; } while (v1*v1 + v2*v2 > 1.0); y=v2/v1; am=ia-1; s=sqrt(2.0*am+1.0); x=s*y+am; } while (x <= 0.0); if (am*log(x/am)-s*y < -700 || v1<0.00001) { goto restart; } e=(1.0+y*y)*exp(am*log(x/am)-s*y); } while (random->uniform() > e); } return x; } /* ------------------------------------------------------------------- returns the sum of n independent gaussian noises squared (i.e. equivalent to summing the square of the return values of nn calls to gasdev) ---------------------------------------------------------------------- */ double FixTempCSVR::sumnoises(int nn) { if (nn == 0) { return 0.0; } else if (nn == 1) { const double rr = random->gaussian(); return rr*rr; } else if (nn % 2 == 0) { return 2.0 * gamdev(nn / 2); } else { const double rr = random->gaussian(); return 2.0 * gamdev((nn-1) / 2) + rr*rr; } } /* ------------------------------------------------------------------- returns the scaling factor for velocities to thermalize the system so it samples the canonical ensemble ---------------------------------------------------------------------- */ double FixTempCSVR::resamplekin(double ekin_old, double ekin_new){ const double tdof = temperature->dof; const double c1 = exp(-update->dt/t_period); const double c2 = (1.0-c1)*ekin_new/ekin_old/tdof; const double r1 = random->gaussian(); const double r2 = sumnoises(tdof - 1); const double scale = c1 + c2*(r1*r1+r2) + 2.0*r1*sqrt(c1*c2); return sqrt(scale); } /* ---------------------------------------------------------------------- */ FixTempCSVR::FixTempCSVR(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), tstr(NULL), id_temp(NULL), random(NULL) { if (narg != 7) error->all(FLERR,"Illegal fix temp/csvr command"); // CSVR thermostat should be applied every step nevery = 1; scalar_flag = 1; global_freq = nevery; dynamic_group_allow = 1; extscalar = 1; tstr = NULL; if (strstr(arg[3],"v_") == arg[3]) { int n = strlen(&arg[3][2]) + 1; tstr = new char[n]; strcpy(tstr,&arg[3][2]); tstyle = EQUAL; } else { t_start = force->numeric(FLERR,arg[3]); t_target = t_start; tstyle = CONSTANT; } t_stop = force->numeric(FLERR,arg[4]); t_period = force->numeric(FLERR,arg[5]); int seed = force->inumeric(FLERR,arg[6]); // error checks if (t_period <= 0.0) error->all(FLERR,"Illegal fix temp/csvr command"); if (seed <= 0) error->all(FLERR,"Illegal fix temp/csvr command"); random = new RanMars(lmp,seed + comm->me); // create a new compute temp style // id = fix-ID + temp, compute group = fix group int n = strlen(id) + 6; id_temp = new char[n]; strcpy(id_temp,id); strcat(id_temp,"_temp"); char **newarg = new char*[3]; newarg[0] = id_temp; newarg[1] = group->names[igroup]; newarg[2] = (char *) "temp"; modify->add_compute(3,newarg); delete [] newarg; tflag = 1; nmax = -1; energy = 0.0; } /* ---------------------------------------------------------------------- */ FixTempCSVR::~FixTempCSVR() { delete [] tstr; // delete temperature if fix created it if (tflag) modify->delete_compute(id_temp); delete [] id_temp; delete random; nmax = -1; } /* ---------------------------------------------------------------------- */ int FixTempCSVR::setmask() { int mask = 0; mask |= END_OF_STEP; mask |= THERMO_ENERGY; return mask; } /* ---------------------------------------------------------------------- */ void FixTempCSVR::init() { // check variable if (tstr) { tvar = input->variable->find(tstr); if (tvar < 0) error->all(FLERR,"Variable name for fix temp/csvr does not exist"); if (input->variable->equalstyle(tvar)) tstyle = EQUAL; else error->all(FLERR,"Variable for fix temp/csvr is invalid style"); } int icompute = modify->find_compute(id_temp); if (icompute < 0) error->all(FLERR,"Temperature ID for fix temp/csvr does not exist"); temperature = modify->compute[icompute]; if (temperature->tempbias) which = BIAS; else which = NOBIAS; } /* ---------------------------------------------------------------------- */ void FixTempCSVR::end_of_step() { // set current t_target // if variable temp, evaluate variable, wrap with clear/add double delta = update->ntimestep - update->beginstep; if (delta != 0.0) delta /= update->endstep - update->beginstep; if (tstyle == CONSTANT) t_target = t_start + delta * (t_stop-t_start); else { modify->clearstep_compute(); t_target = input->variable->compute_equal(tvar); if (t_target < 0.0) error->one(FLERR, "Fix temp/csvr variable returned negative temperature"); modify->addstep_compute(update->ntimestep + nevery); } const double t_current = temperature->compute_scalar(); const double efactor = 0.5 * temperature->dof * force->boltz; const double ekin_old = t_current * efactor; const double ekin_new = t_target * efactor; // there is nothing to do, if there are no degrees of freedom if (temperature->dof < 1) return; // compute velocity scaling factor on root node and broadcast double lamda; if (comm->me == 0) { lamda = resamplekin(ekin_old, ekin_new); } MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world); double * const * const v = atom->v; const int * const mask = atom->mask; const int nlocal = atom->nlocal; if (which == NOBIAS) { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { v[i][0] *= lamda; v[i][1] *= lamda; v[i][2] *= lamda; } } } else { for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { temperature->remove_bias(i,v[i]); v[i][0] *= lamda; v[i][1] *= lamda; v[i][2] *= lamda; temperature->restore_bias(i,v[i]); } } } // tally the kinetic energy transferred between heat bath and system energy += ekin_old * (1.0 - lamda*lamda); } /* ---------------------------------------------------------------------- */ int FixTempCSVR::modify_param(int narg, char **arg) { if (strcmp(arg[0],"temp") == 0) { if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); if (tflag) { modify->delete_compute(id_temp); tflag = 0; } delete [] id_temp; int n = strlen(arg[1]) + 1; id_temp = new char[n]; strcpy(id_temp,arg[1]); int icompute = modify->find_compute(id_temp); if (icompute < 0) error->all(FLERR,"Could not find fix_modify temperature ID"); temperature = modify->compute[icompute]; if (temperature->tempflag == 0) error->all(FLERR, "Fix_modify temperature ID does not compute temperature"); if (temperature->igroup != igroup && comm->me == 0) error->warning(FLERR,"Group for fix_modify temp != fix group"); return 2; } return 0; } /* ---------------------------------------------------------------------- */ void FixTempCSVR::reset_target(double t_new) { t_target = t_start = t_stop = t_new; } /* ---------------------------------------------------------------------- */ double FixTempCSVR::compute_scalar() { return energy; } /* ---------------------------------------------------------------------- extract thermostat properties ------------------------------------------------------------------------- */ void *FixTempCSVR::extract(const char *str, int &dim) { dim=0; if (strcmp(str,"t_target") == 0) { return &t_target; } return NULL; }