diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp
index 6a376f20f..ec570d22e 100644
--- a/src/compute_temp_sphere.cpp
+++ b/src/compute_temp_sphere.cpp
@@ -1,329 +1,330 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "compute_temp_sphere.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{ROTATE,ALL};
#define INERTIA 0.4 // moment of inertia prefactor for sphere
/* ---------------------------------------------------------------------- */
ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all(FLERR,"Illegal compute temp/sphere command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 0;
id_bias = NULL;
mode = ALL;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/sphere command");
tempbias = 1;
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"dof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal compute temp/sphere command");
if (strcmp(arg[iarg+1],"rotate") == 0) mode = ROTATE;
else if (strcmp(arg[iarg+1],"all") == 0) mode = ALL;
else error->all(FLERR,"Illegal compute temp/sphere command");
iarg += 2;
} else error->all(FLERR,"Illegal compute temp/sphere command");
}
vector = new double[6];
// error checks
if (!atom->sphere_flag)
error->all(FLERR,"Compute temp/sphere requires atom style sphere");
}
/* ---------------------------------------------------------------------- */
ComputeTempSphere::~ComputeTempSphere()
{
delete [] id_bias;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::init()
{
if (tempbias) {
int i = modify->find_compute(id_bias);
if (i < 0)
error->all(FLERR,"Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
if (tbias->igroup != igroup)
error->all(FLERR,"Bias compute group does not match compute group");
tbias->init();
+ tbias->setup();
if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
else tempbias = 1;
}
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::setup()
{
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::dof_compute()
{
int count,count_all;
// 6 or 3 dof for extended/point particles for 3d
// 3 or 2 dof for extended/point particles for 2d
// which dof are included also depends on mode
// assume full rotation of extended particles
// user should correct this via compute_modify if needed
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
count = 0;
if (domain->dimension == 3) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 3;
} else {
if (mode == ALL) count += 6;
else count += 3;
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 2;
} else {
if (mode == ALL) count += 3;
else count += 1;
}
}
}
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof = count_all;
// additional adjustments to dof
if (tempbias == 1) {
if (mode == ALL) {
double natoms = group->count(igroup);
dof -= tbias->dof_remove(-1) * natoms;
}
} else if (tempbias == 2) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
count = 0;
if (domain->dimension == 3) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 3;
} else {
if (mode == ALL) count += 6;
else count += 3;
}
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (radius[i] == 0.0) {
if (mode == ALL) count += 2;
} else {
if (mode == ALL) count += 3;
else count += 1;
}
}
}
}
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof -= count_all;
}
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempSphere::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *radius = atom->radius;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// point particles will not contribute rotation due to radius = 0
double t = 0.0;
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * INERTIA*rmass[i]*radius[i]*radius[i];
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tempbias == 2) dof_compute();
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::compute_vector()
{
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *rmass = atom->rmass;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// point particles will not contribute rotation due to radius = 0
double massone,inertiaone,t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
if (mode == ALL) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[i];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
t[0] += inertiaone * omega[i][0]*omega[i][0];
t[1] += inertiaone * omega[i][1]*omega[i][1];
t[2] += inertiaone * omega[i][2]*omega[i][2];
t[3] += inertiaone * omega[i][0]*omega[i][1];
t[4] += inertiaone * omega[i][0]*omega[i][2];
t[5] += inertiaone * omega[i][1]*omega[i][2];
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
inertiaone = INERTIA*rmass[i]*radius[i]*radius[i];
t[0] += inertiaone * omega[i][0]*omega[i][0];
t[1] += inertiaone * omega[i][1]*omega[i][1];
t[2] += inertiaone * omega[i][2]*omega[i][2];
t[3] += inertiaone * omega[i][0]*omega[i][1];
t[4] += inertiaone * omega[i][0]*omega[i][2];
t[5] += inertiaone * omega[i][1]*omega[i][2];
}
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias(int i, double *v)
{
tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias(int i, double *v)
{
tbias->restore_bias(i,v);
}
diff --git a/src/modify.cpp b/src/modify.cpp
index 47b382116..9c843b8ab 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -1,1197 +1,1198 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "stdio.h"
#include "string.h"
#include "modify.h"
#include "style_compute.h"
#include "style_fix.h"
#include "atom.h"
#include "comm.h"
#include "fix.h"
#include "compute.h"
#include "group.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define DELTA 4
#define BIG 1.0e20
#define NEXCEPT 3 // change when add to exceptions in add_fix()
/* ---------------------------------------------------------------------- */
Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
{
nfix = maxfix = 0;
n_initial_integrate = n_post_integrate = 0;
n_pre_exchange = n_pre_neighbor = 0;
n_pre_force = n_post_force = 0;
n_final_integrate = n_end_of_step = n_thermo_energy = 0;
n_initial_integrate_respa = n_post_integrate_respa = 0;
n_pre_force_respa = n_post_force_respa = n_final_integrate_respa = 0;
n_min_pre_exchange = n_min_pre_force = n_min_post_force = n_min_energy = 0;
fix = NULL;
fmask = NULL;
list_initial_integrate = list_post_integrate = NULL;
list_pre_exchange = list_pre_neighbor = NULL;
list_pre_force = list_post_force = NULL;
list_final_integrate = list_end_of_step = NULL;
list_thermo_energy = NULL;
list_initial_integrate_respa = list_post_integrate_respa = NULL;
list_pre_force_respa = list_post_force_respa = NULL;
list_final_integrate_respa = NULL;
list_min_pre_exchange = list_min_pre_neighbor = NULL;
list_min_pre_force = list_min_post_force = NULL;
list_min_energy = NULL;
end_of_step_every = NULL;
list_timeflag = NULL;
nfix_restart_global = 0;
id_restart_global = style_restart_global = state_restart_global = NULL;
nfix_restart_peratom = 0;
id_restart_peratom = style_restart_peratom = NULL;
index_restart_peratom = NULL;
ncompute = maxcompute = 0;
compute = NULL;
}
/* ---------------------------------------------------------------------- */
Modify::~Modify()
{
// delete all fixes
// do it via delete_fix() so callbacks in Atom are also updated correctly
while (nfix) delete_fix(fix[0]->id);
memory->sfree(fix);
memory->destroy(fmask);
// delete all computes
for (int i = 0; i < ncompute; i++) delete compute[i];
memory->sfree(compute);
delete [] list_initial_integrate;
delete [] list_post_integrate;
delete [] list_pre_exchange;
delete [] list_pre_neighbor;
delete [] list_pre_force;
delete [] list_post_force;
delete [] list_final_integrate;
delete [] list_end_of_step;
delete [] list_thermo_energy;
delete [] list_initial_integrate_respa;
delete [] list_post_integrate_respa;
delete [] list_pre_force_respa;
delete [] list_post_force_respa;
delete [] list_final_integrate_respa;
delete [] list_min_pre_exchange;
delete [] list_min_pre_neighbor;
delete [] list_min_pre_force;
delete [] list_min_post_force;
delete [] list_min_energy;
delete [] end_of_step_every;
delete [] list_timeflag;
restart_deallocate();
}
/* ----------------------------------------------------------------------
initialize all fixes and computes
------------------------------------------------------------------------- */
void Modify::init()
{
int i,j;
// delete storage of restart info since it is not valid after 1st run
restart_deallocate();
// create lists of fixes to call at each stage of run
list_init(INITIAL_INTEGRATE,n_initial_integrate,list_initial_integrate);
list_init(POST_INTEGRATE,n_post_integrate,list_post_integrate);
list_init(PRE_EXCHANGE,n_pre_exchange,list_pre_exchange);
list_init(PRE_NEIGHBOR,n_pre_neighbor,list_pre_neighbor);
list_init(PRE_FORCE,n_pre_force,list_pre_force);
list_init(POST_FORCE,n_post_force,list_post_force);
list_init(FINAL_INTEGRATE,n_final_integrate,list_final_integrate);
list_init_end_of_step(END_OF_STEP,n_end_of_step,list_end_of_step);
list_init_thermo_energy(THERMO_ENERGY,n_thermo_energy,list_thermo_energy);
list_init(INITIAL_INTEGRATE_RESPA,
n_initial_integrate_respa,list_initial_integrate_respa);
list_init(POST_INTEGRATE_RESPA,
n_post_integrate_respa,list_post_integrate_respa);
list_init(POST_FORCE_RESPA,
n_post_force_respa,list_post_force_respa);
list_init(PRE_FORCE_RESPA,
n_pre_force_respa,list_pre_force_respa);
list_init(FINAL_INTEGRATE_RESPA,
n_final_integrate_respa,list_final_integrate_respa);
list_init(MIN_PRE_EXCHANGE,n_min_pre_exchange,list_min_pre_exchange);
list_init(MIN_PRE_NEIGHBOR,n_min_pre_neighbor,list_min_pre_neighbor);
list_init(MIN_PRE_FORCE,n_min_pre_force,list_min_pre_force);
list_init(MIN_POST_FORCE,n_min_post_force,list_min_post_force);
list_init(MIN_ENERGY,n_min_energy,list_min_energy);
// init each fix
// needs to come before compute init
// this is b/c some computes call fix->dof()
// FixRigid::dof() depends on its own init having been called
+ // NOTE: 2/13, this may no longer be needed b/c computes do dof in setup()
for (i = 0; i < nfix; i++) fix[i]->init();
// set global flag if any fix has its restart_pbc flag set
restart_pbc_any = 0;
for (i = 0; i < nfix; i++)
if (fix[i]->restart_pbc) restart_pbc_any = 1;
// create list of computes that store invocation times
list_init_compute();
// init each compute
// set invoked_scalar,vector,etc to -1 to force new run to re-compute them
// add initial timestep to all computes that store invocation times
// since any of them may be invoked by initial thermo
// do not clear out invocation times stored within a compute,
// b/c some may be holdovers from previous run, like for ave fixes
for (i = 0; i < ncompute; i++) {
compute[i]->init();
compute[i]->invoked_scalar = -1;
compute[i]->invoked_vector = -1;
compute[i]->invoked_array = -1;
compute[i]->invoked_peratom = -1;
compute[i]->invoked_local = -1;
}
addstep_compute_all(update->ntimestep);
// warn if any particle is time integrated more than once
int nlocal = atom->nlocal;
int *mask = atom->mask;
int *flag = new int[nlocal];
for (i = 0; i < nlocal; i++) flag[i] = 0;
int groupbit;
for (i = 0; i < nfix; i++) {
if (fix[i]->time_integrate == 0) continue;
groupbit = fix[i]->groupbit;
for (j = 0; j < nlocal; j++)
if (mask[j] & groupbit) flag[j]++;
}
int check = 0;
for (i = 0; i < nlocal; i++)
if (flag[i] > 1) check = 1;
delete [] flag;
int checkall;
MPI_Allreduce(&check,&checkall,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0 && checkall)
error->warning(FLERR,
"One or more atoms are time integrated more than once");
}
/* ----------------------------------------------------------------------
setup for run, calls setup() of all fixes and computes
called from Verlet, RESPA, Min
------------------------------------------------------------------------- */
void Modify::setup(int vflag)
{
if (update->whichflag == 1)
for (int i = 0; i < nfix; i++) fix[i]->setup(vflag);
else if (update->whichflag == 2)
for (int i = 0; i < nfix; i++) fix[i]->min_setup(vflag);
// call computes after fixes
// fix rigid dof() can't be called by temperature computes at init
for (int i = 0; i < ncompute; i++) compute[i]->setup();
}
/* ----------------------------------------------------------------------
setup pre_exchange call, only for fixes that define pre_exchange
called from Verlet, RESPA, Min, and WriteRestart with whichflag = 0
------------------------------------------------------------------------- */
void Modify::setup_pre_exchange()
{
if (update->whichflag <= 1)
for (int i = 0; i < n_pre_exchange; i++)
fix[list_pre_exchange[i]]->setup_pre_exchange();
else if (update->whichflag == 2)
for (int i = 0; i < n_min_pre_exchange; i++)
fix[list_min_pre_exchange[i]]->min_setup_pre_exchange();
}
/* ----------------------------------------------------------------------
setup pre_neighbor call, only for fixes that define pre_neighbor
called from Verlet, RESPA
------------------------------------------------------------------------- */
void Modify::setup_pre_neighbor()
{
if (update->whichflag == 1)
for (int i = 0; i < n_pre_neighbor; i++)
fix[list_pre_neighbor[i]]->setup_pre_neighbor();
else if (update->whichflag == 2)
for (int i = 0; i < n_pre_neighbor; i++)
fix[list_min_pre_neighbor[i]]->min_setup_pre_neighbor();
}
/* ----------------------------------------------------------------------
setup pre_force call, only for fixes that define pre_force
called from Verlet, RESPA, Min
------------------------------------------------------------------------- */
void Modify::setup_pre_force(int vflag)
{
if (update->whichflag == 1)
for (int i = 0; i < n_pre_force; i++)
fix[list_pre_force[i]]->setup_pre_force(vflag);
else if (update->whichflag == 2)
for (int i = 0; i < n_min_pre_force; i++)
fix[list_min_pre_force[i]]->min_setup_pre_force(vflag);
}
/* ----------------------------------------------------------------------
1st half of integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::initial_integrate(int vflag)
{
for (int i = 0; i < n_initial_integrate; i++)
fix[list_initial_integrate[i]]->initial_integrate(vflag);
}
/* ----------------------------------------------------------------------
post_integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_integrate()
{
for (int i = 0; i < n_post_integrate; i++)
fix[list_post_integrate[i]]->post_integrate();
}
/* ----------------------------------------------------------------------
pre_exchange call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::pre_exchange()
{
for (int i = 0; i < n_pre_exchange; i++)
fix[list_pre_exchange[i]]->pre_exchange();
}
/* ----------------------------------------------------------------------
pre_neighbor call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::pre_neighbor()
{
for (int i = 0; i < n_pre_neighbor; i++)
fix[list_pre_neighbor[i]]->pre_neighbor();
}
/* ----------------------------------------------------------------------
pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::pre_force(int vflag)
{
for (int i = 0; i < n_pre_force; i++)
fix[list_pre_force[i]]->pre_force(vflag);
}
/* ----------------------------------------------------------------------
post_force call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_force(int vflag)
{
for (int i = 0; i < n_post_force; i++)
fix[list_post_force[i]]->post_force(vflag);
}
/* ----------------------------------------------------------------------
2nd half of integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::final_integrate()
{
for (int i = 0; i < n_final_integrate; i++)
fix[list_final_integrate[i]]->final_integrate();
}
/* ----------------------------------------------------------------------
end-of-timestep call, only for relevant fixes
only call fix->end_of_step() on timesteps that are multiples of nevery
------------------------------------------------------------------------- */
void Modify::end_of_step()
{
for (int i = 0; i < n_end_of_step; i++)
if (update->ntimestep % end_of_step_every[i] == 0)
fix[list_end_of_step[i]]->end_of_step();
}
/* ----------------------------------------------------------------------
thermo energy call, only for relevant fixes
called by Thermo class
compute_scalar() is fix call to return energy
------------------------------------------------------------------------- */
double Modify::thermo_energy()
{
double energy = 0.0;
for (int i = 0; i < n_thermo_energy; i++)
energy += fix[list_thermo_energy[i]]->compute_scalar();
return energy;
}
/* ----------------------------------------------------------------------
post_run call
------------------------------------------------------------------------- */
void Modify::post_run()
{
for (int i = 0; i < nfix; i++) fix[i]->post_run();
}
/* ----------------------------------------------------------------------
setup rRESPA pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::setup_pre_force_respa(int vflag, int ilevel)
{
for (int i = 0; i < n_pre_force; i++)
fix[list_pre_force[i]]->setup_pre_force_respa(vflag,ilevel);
}
/* ----------------------------------------------------------------------
1st half of rRESPA integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::initial_integrate_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_initial_integrate_respa; i++)
fix[list_initial_integrate_respa[i]]->
initial_integrate_respa(vflag,ilevel,iloop);
}
/* ----------------------------------------------------------------------
rRESPA post_integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_integrate_respa(int ilevel, int iloop)
{
for (int i = 0; i < n_post_integrate_respa; i++)
fix[list_post_integrate_respa[i]]->post_integrate_respa(ilevel,iloop);
}
/* ----------------------------------------------------------------------
rRESPA pre_force call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::pre_force_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_pre_force_respa; i++)
fix[list_pre_force_respa[i]]->pre_force_respa(vflag,ilevel,iloop);
}
/* ----------------------------------------------------------------------
rRESPA post_force call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_force_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_post_force_respa; i++)
fix[list_post_force_respa[i]]->post_force_respa(vflag,ilevel,iloop);
}
/* ----------------------------------------------------------------------
2nd half of rRESPA integrate call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::final_integrate_respa(int ilevel, int iloop)
{
for (int i = 0; i < n_final_integrate_respa; i++)
fix[list_final_integrate_respa[i]]->final_integrate_respa(ilevel,iloop);
}
/* ----------------------------------------------------------------------
minimizer pre-exchange call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_pre_exchange()
{
for (int i = 0; i < n_min_pre_exchange; i++)
fix[list_min_pre_exchange[i]]->min_pre_exchange();
}
/* ----------------------------------------------------------------------
minimizer pre-neighbor call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_pre_neighbor()
{
for (int i = 0; i < n_min_pre_neighbor; i++)
fix[list_min_pre_neighbor[i]]->min_pre_neighbor();
}
/* ----------------------------------------------------------------------
minimizer pre-force call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_pre_force(int vflag)
{
for (int i = 0; i < n_min_pre_force; i++)
fix[list_min_pre_force[i]]->min_pre_force(vflag);
}
/* ----------------------------------------------------------------------
minimizer force adjustment call, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_post_force(int vflag)
{
for (int i = 0; i < n_min_post_force; i++)
fix[list_min_post_force[i]]->min_post_force(vflag);
}
/* ----------------------------------------------------------------------
minimizer energy/force evaluation, only for relevant fixes
return energy and forces on extra degrees of freedom
------------------------------------------------------------------------- */
double Modify::min_energy(double *fextra)
{
int ifix,index;
index = 0;
double eng = 0.0;
for (int i = 0; i < n_min_energy; i++) {
ifix = list_min_energy[i];
eng += fix[ifix]->min_energy(&fextra[index]);
index += fix[ifix]->min_dof();
}
return eng;
}
/* ----------------------------------------------------------------------
store current state of extra dof, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_store()
{
for (int i = 0; i < n_min_energy; i++)
fix[list_min_energy[i]]->min_store();
}
/* ----------------------------------------------------------------------
mange state of extra dof on a stack, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_clearstore()
{
for (int i = 0; i < n_min_energy; i++)
fix[list_min_energy[i]]->min_clearstore();
}
void Modify::min_pushstore()
{
for (int i = 0; i < n_min_energy; i++)
fix[list_min_energy[i]]->min_pushstore();
}
void Modify::min_popstore()
{
for (int i = 0; i < n_min_energy; i++)
fix[list_min_energy[i]]->min_popstore();
}
/* ----------------------------------------------------------------------
displace extra dof along vector hextra, only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_step(double alpha, double *hextra)
{
int ifix,index;
index = 0;
for (int i = 0; i < n_min_energy; i++) {
ifix = list_min_energy[i];
fix[ifix]->min_step(alpha,&hextra[index]);
index += fix[ifix]->min_dof();
}
}
/* ----------------------------------------------------------------------
compute max allowed step size along vector hextra, only for relevant fixes
------------------------------------------------------------------------- */
double Modify::max_alpha(double *hextra)
{
int ifix,index;
double alpha = BIG;
index = 0;
for (int i = 0; i < n_min_energy; i++) {
ifix = list_min_energy[i];
double alpha_one = fix[ifix]->max_alpha(&hextra[index]);
alpha = MIN(alpha,alpha_one);
index += fix[ifix]->min_dof();
}
return alpha;
}
/* ----------------------------------------------------------------------
extract extra dof for minimization, only for relevant fixes
------------------------------------------------------------------------- */
int Modify::min_dof()
{
int ndof = 0;
for (int i = 0; i < n_min_energy; i++)
ndof += fix[list_min_energy[i]]->min_dof();
return ndof;
}
/* ----------------------------------------------------------------------
reset reference state of fix, only for relevant fixes
------------------------------------------------------------------------- */
int Modify::min_reset_ref()
{
int itmp,itmpall;
itmpall = 0;
for (int i = 0; i < n_min_energy; i++) {
itmp = fix[list_min_energy[i]]->min_reset_ref();
if (itmp) itmpall = 1;
}
return itmpall;
}
/* ----------------------------------------------------------------------
add a new fix or replace one with same ID
------------------------------------------------------------------------- */
void Modify::add_fix(int narg, char **arg, char *suffix)
{
const char *exceptions[NEXCEPT] = {"GPU","OMP","cmap"};
if (narg < 3) error->all(FLERR,"Illegal fix command");
// cannot define fix before box exists unless style is in exception list
// don't like this way of checking for exceptions by adding fixes to list,
// but can't think of better way
// too late if instantiate fix, then check flag set in fix constructor,
// since some fixes access domain settings in their constructor
if (domain->box_exist == 0) {
int m;
for (m = 0; m < NEXCEPT; m++)
if (strcmp(arg[2],exceptions[m]) == 0) break;
if (m == NEXCEPT)
error->all(FLERR,"Fix command before simulation box is defined");
}
// check group ID
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
// if fix ID exists:
// set newflag = 0 so create new fix in same location in fix list
// error if new style does not match old style
// since can't replace it (all when-to-invoke ptrs would be invalid)
// warn if new group != old group
// delete old fix, but do not call update_callback(),
// since will replace this fix and thus other fix locs will not change
// set ptr to NULL in case new fix scans list of fixes,
// e.g. scan will occur in add_callback() if called by new fix
// if fix ID does not exist:
// set newflag = 1 so create new fix
// extend fix and fmask lists as necessary
int ifix,newflag;
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(arg[0],fix[ifix]->id) == 0) break;
if (ifix < nfix) {
newflag = 0;
if (strcmp(arg[2],fix[ifix]->style) != 0)
error->all(FLERR,"Replacing a fix, but new style != old style");
if (fix[ifix]->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Replacing a fix, but new group != old group");
delete fix[ifix];
fix[ifix] = NULL;
} else {
newflag = 1;
if (nfix == maxfix) {
maxfix += DELTA;
fix = (Fix **) memory->srealloc(fix,maxfix*sizeof(Fix *),"modify:fix");
memory->grow(fmask,maxfix,"modify:fmask");
}
}
// create the Fix, first with suffix appended
int success = 0;
if (suffix && lmp->suffix_enable) {
char estyle[256];
sprintf(estyle,"%s/%s",arg[2],suffix);
success = 1;
if (0) return;
#define FIX_CLASS
#define FixStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) fix[ifix] = new Class(lmp,narg,arg);
#include "style_fix.h"
#undef FixStyle
#undef FIX_CLASS
else success = 0;
}
if (!success) {
if (0) return;
#define FIX_CLASS
#define FixStyle(key,Class) \
else if (strcmp(arg[2],#key) == 0) fix[ifix] = new Class(lmp,narg,arg);
#include "style_fix.h"
#undef FixStyle
#undef FIX_CLASS
else error->all(FLERR,"Invalid fix style");
}
// set fix mask values and increment nfix (if new)
fmask[ifix] = fix[ifix]->setmask();
if (newflag) nfix++;
// check if Fix is in restart_global list
// if yes, pass state info to the Fix so it can reset itself
for (int i = 0; i < nfix_restart_global; i++)
if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
fix[ifix]->restart(state_restart_global[i]);
if (comm->me == 0) {
char *str = (char *) ("Resetting global state of Fix %s Style %s "
"from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
// check if Fix is in restart_peratom list
// if yes, loop over atoms so they can extract info from atom->extra array
for (int i = 0; i < nfix_restart_peratom; i++)
if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
for (int j = 0; j < atom->nlocal; j++)
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
if (comm->me == 0) {
char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
"from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
}
/* ----------------------------------------------------------------------
modify a Fix's parameters
------------------------------------------------------------------------- */
void Modify::modify_fix(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
// lookup Fix ID
int ifix;
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(arg[0],fix[ifix]->id) == 0) break;
if (ifix == nfix) error->all(FLERR,"Could not find fix_modify ID");
fix[ifix]->modify_params(narg-1,&arg[1]);
}
/* ----------------------------------------------------------------------
delete a Fix from list of Fixes
Atom class must update indices in its list of callbacks to fixes
------------------------------------------------------------------------- */
void Modify::delete_fix(const char *id)
{
int ifix = find_fix(id);
if (ifix < 0) error->all(FLERR,"Could not find fix ID to delete");
delete fix[ifix];
atom->update_callback(ifix);
// move other Fixes and fmask down in list one slot
for (int i = ifix+1; i < nfix; i++) fix[i-1] = fix[i];
for (int i = ifix+1; i < nfix; i++) fmask[i-1] = fmask[i];
nfix--;
}
/* ----------------------------------------------------------------------
find a fix by ID
return index of fix or -1 if not found
------------------------------------------------------------------------- */
int Modify::find_fix(const char *id)
{
int ifix;
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(id,fix[ifix]->id) == 0) break;
if (ifix == nfix) return -1;
return ifix;
}
/* ----------------------------------------------------------------------
add a new compute
------------------------------------------------------------------------- */
void Modify::add_compute(int narg, char **arg, char *suffix)
{
if (narg < 3) error->all(FLERR,"Illegal compute command");
// error check
for (int icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0)
error->all(FLERR,"Reuse of compute ID");
// extend Compute list if necessary
if (ncompute == maxcompute) {
maxcompute += DELTA;
compute = (Compute **)
memory->srealloc(compute,maxcompute*sizeof(Compute *),"modify:compute");
}
// create the Compute, first with suffix appended
int success = 0;
if (suffix && lmp->suffix_enable) {
char estyle[256];
sprintf(estyle,"%s/%s",arg[2],suffix);
success = 1;
if (0) return;
#define COMPUTE_CLASS
#define ComputeStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) \
compute[ncompute] = new Class(lmp,narg,arg);
#include "style_compute.h"
#undef ComputeStyle
#undef COMPUTE_CLASS
else success = 0;
}
if (!success) {
if (0) return;
#define COMPUTE_CLASS
#define ComputeStyle(key,Class) \
else if (strcmp(arg[2],#key) == 0) \
compute[ncompute] = new Class(lmp,narg,arg);
#include "style_compute.h"
#undef ComputeStyle
#undef COMPUTE_CLASS
else error->all(FLERR,"Invalid compute style");
}
ncompute++;
}
/* ----------------------------------------------------------------------
modify a Compute's parameters
------------------------------------------------------------------------- */
void Modify::modify_compute(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal compute_modify command");
// lookup Compute ID
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0) break;
if (icompute == ncompute) error->all(FLERR,"Could not find compute_modify ID");
compute[icompute]->modify_params(narg-1,&arg[1]);
}
/* ----------------------------------------------------------------------
delete a Compute from list of Computes
------------------------------------------------------------------------- */
void Modify::delete_compute(const char *id)
{
int icompute = find_compute(id);
if (icompute < 0) error->all(FLERR,"Could not find compute ID to delete");
delete compute[icompute];
// move other Computes down in list one slot
for (int i = icompute+1; i < ncompute; i++) compute[i-1] = compute[i];
ncompute--;
}
/* ----------------------------------------------------------------------
find a compute by ID
return index of compute or -1 if not found
------------------------------------------------------------------------- */
int Modify::find_compute(const char *id)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(id,compute[icompute]->id) == 0) break;
if (icompute == ncompute) return -1;
return icompute;
}
/* ----------------------------------------------------------------------
clear invoked flag of all computes
called everywhere that computes are used, before computes are invoked
invoked flag used to avoid re-invoking same compute multiple times
and to flag computes that store invocation times as having been invoked
------------------------------------------------------------------------- */
void Modify::clearstep_compute()
{
for (int icompute = 0; icompute < ncompute; icompute++)
compute[icompute]->invoked_flag = 0;
}
/* ----------------------------------------------------------------------
loop over computes that store invocation times
if its invoked flag set on this timestep, schedule next invocation
called everywhere that computes are used, after computes are invoked
------------------------------------------------------------------------- */
void Modify::addstep_compute(bigint newstep)
{
for (int icompute = 0; icompute < n_timeflag; icompute++)
if (compute[list_timeflag[icompute]]->invoked_flag)
compute[list_timeflag[icompute]]->addstep(newstep);
}
/* ----------------------------------------------------------------------
loop over all computes
schedule next invocation for those that store invocation times
called when not sure what computes will be needed on newstep
do not loop only over n_timeflag, since may not be set yet
------------------------------------------------------------------------- */
void Modify::addstep_compute_all(bigint newstep)
{
for (int icompute = 0; icompute < ncompute; icompute++)
if (compute[icompute]->timeflag) compute[icompute]->addstep(newstep);
}
/* ----------------------------------------------------------------------
write to restart file for all Fixes with restart info
(1) fixes that have global state
(2) fixes that store per-atom quantities
------------------------------------------------------------------------- */
void Modify::write_restart(FILE *fp)
{
int me = comm->me;
int count = 0;
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
int n;
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) {
if (me == 0) {
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
}
fix[i]->write_restart(fp);
}
count = 0;
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) {
if (me == 0) {
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
n = fix[i]->maxsize_restart();
fwrite(&n,sizeof(int),1,fp);
}
}
}
/* ----------------------------------------------------------------------
read in restart file data on all previously defined Fixes with restart info
(1) fixes that have global state
(2) fixes that store per-atom quantities
return maxsize of extra info that will be stored with any atom
------------------------------------------------------------------------- */
int Modify::read_restart(FILE *fp)
{
// nfix_restart_global = # of restart entries with global state info
int me = comm->me;
if (me == 0) fread(&nfix_restart_global,sizeof(int),1,fp);
MPI_Bcast(&nfix_restart_global,1,MPI_INT,0,world);
// allocate space for each entry
if (nfix_restart_global) {
id_restart_global = new char*[nfix_restart_global];
style_restart_global = new char*[nfix_restart_global];
state_restart_global = new char*[nfix_restart_global];
}
// read each entry and Bcast to all procs
// each entry has id string, style string, chunk of state data
int n;
for (int i = 0; i < nfix_restart_global; i++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
id_restart_global[i] = new char[n];
if (me == 0) fread(id_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(id_restart_global[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style_restart_global[i] = new char[n];
if (me == 0) fread(style_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(style_restart_global[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
state_restart_global[i] = new char[n];
if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);
}
// nfix_restart_peratom = # of restart entries with peratom info
int maxsize = 0;
if (me == 0) fread(&nfix_restart_peratom,sizeof(int),1,fp);
MPI_Bcast(&nfix_restart_peratom,1,MPI_INT,0,world);
// allocate space for each entry
if (nfix_restart_peratom) {
id_restart_peratom = new char*[nfix_restart_peratom];
style_restart_peratom = new char*[nfix_restart_peratom];
index_restart_peratom = new int[nfix_restart_peratom];
}
// read each entry and Bcast to all procs
// each entry has id string, style string, maxsize of one atom's data
// set index = which set of extra data this fix represents
for (int i = 0; i < nfix_restart_peratom; i++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
id_restart_peratom[i] = new char[n];
if (me == 0) fread(id_restart_peratom[i],sizeof(char),n,fp);
MPI_Bcast(id_restart_peratom[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style_restart_peratom[i] = new char[n];
if (me == 0) fread(style_restart_peratom[i],sizeof(char),n,fp);
MPI_Bcast(style_restart_peratom[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
maxsize += n;
index_restart_peratom[i] = i;
}
return maxsize;
}
/* ----------------------------------------------------------------------
delete all lists of restart file Fix info
------------------------------------------------------------------------- */
void Modify::restart_deallocate()
{
if (nfix_restart_global) {
for (int i = 0; i < nfix_restart_global; i++) {
delete [] id_restart_global[i];
delete [] style_restart_global[i];
delete [] state_restart_global[i];
}
delete [] id_restart_global;
delete [] style_restart_global;
delete [] state_restart_global;
}
if (nfix_restart_peratom) {
for (int i = 0; i < nfix_restart_peratom; i++) {
delete [] id_restart_peratom[i];
delete [] style_restart_peratom[i];
}
delete [] id_restart_peratom;
delete [] style_restart_peratom;
delete [] index_restart_peratom;
}
nfix_restart_global = nfix_restart_peratom = 0;
}
/* ----------------------------------------------------------------------
create list of fix indices for fixes which match mask
------------------------------------------------------------------------- */
void Modify::list_init(int mask, int &n, int *&list)
{
delete [] list;
n = 0;
for (int i = 0; i < nfix; i++) if (fmask[i] & mask) n++;
list = new int[n];
n = 0;
for (int i = 0; i < nfix; i++) if (fmask[i] & mask) list[n++] = i;
}
/* ----------------------------------------------------------------------
create list of fix indices for end_of_step fixes
also create end_of_step_every[]
------------------------------------------------------------------------- */
void Modify::list_init_end_of_step(int mask, int &n, int *&list)
{
delete [] list;
delete [] end_of_step_every;
n = 0;
for (int i = 0; i < nfix; i++) if (fmask[i] & mask) n++;
list = new int[n];
end_of_step_every = new int[n];
n = 0;
for (int i = 0; i < nfix; i++)
if (fmask[i] & mask) {
list[n] = i;
end_of_step_every[n++] = fix[i]->nevery;
}
}
/* ----------------------------------------------------------------------
create list of fix indices for thermo energy fixes
only added to list if fix has THERMO_ENERGY mask
and its thermo_energy flag was set via fix_modify
------------------------------------------------------------------------- */
void Modify::list_init_thermo_energy(int mask, int &n, int *&list)
{
delete [] list;
n = 0;
for (int i = 0; i < nfix; i++)
if (fmask[i] & mask && fix[i]->thermo_energy) n++;
list = new int[n];
n = 0;
for (int i = 0; i < nfix; i++)
if (fmask[i] & mask && fix[i]->thermo_energy) list[n++] = i;
}
/* ----------------------------------------------------------------------
create list of compute indices for computes which store invocation times
------------------------------------------------------------------------- */
void Modify::list_init_compute()
{
delete [] list_timeflag;
n_timeflag = 0;
for (int i = 0; i < ncompute; i++)
if (compute[i]->timeflag) n_timeflag++;
list_timeflag = new int[n_timeflag];
n_timeflag = 0;
for (int i = 0; i < ncompute; i++)
if (compute[i]->timeflag) list_timeflag[n_timeflag++] = i;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory from all fixes
------------------------------------------------------------------------- */
bigint Modify::memory_usage()
{
bigint bytes = 0;
for (int i = 0; i < nfix; i++)
bytes += static_cast<bigint> (fix[i]->memory_usage());
for (int i = 0; i < ncompute; i++)
bytes += static_cast<bigint> (compute[i]->memory_usage());
return bytes;
}
diff --git a/src/velocity.cpp b/src/velocity.cpp
index e69b6d67a..eb64b8cc9 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -1,797 +1,799 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "velocity.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "lattice.h"
#include "input.h"
#include "variable.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "compute_temp.h"
#include "random_park.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{CREATE,SET,SCALE,RAMP,ZERO};
enum{ALL,LOCAL,GEOM};
enum{NONE,CONSTANT,EQUAL,ATOM};
#define WARMUP 100
#define SMALL 0.001
/* ---------------------------------------------------------------------- */
Velocity::Velocity(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void Velocity::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal velocity command");
if (domain->box_exist == 0)
error->all(FLERR,"Velocity command before simulation box is defined");
if (atom->natoms == 0)
error->all(FLERR,"Velocity command with no atoms existing");
// atom masses must all be set
atom->check_mass();
// identify group
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find velocity group ID");
groupbit = group->bitmask[igroup];
// identify style
if (strcmp(arg[1],"create") == 0) style = CREATE;
else if (strcmp(arg[1],"set") == 0) style = SET;
else if (strcmp(arg[1],"scale") == 0) style = SCALE;
else if (strcmp(arg[1],"ramp") == 0) style = RAMP;
else if (strcmp(arg[1],"zero") == 0) style = ZERO;
else error->all(FLERR,"Illegal velocity command");
// set defaults
temperature = NULL;
dist_flag = 0;
sum_flag = 0;
momentum_flag = 1;
rotation_flag = 0;
loop_flag = ALL;
scale_flag = 1;
// read options from end of input line
// change defaults as options specify
if (style == CREATE) options(narg-4,&arg[4]);
else if (style == SET) options(narg-5,&arg[5]);
else if (style == SCALE) options(narg-3,&arg[3]);
else if (style == RAMP) options(narg-8,&arg[8]);
else if (style == ZERO) options(narg-3,&arg[3]);
// initialize velocities based on style
// create() invoked differently, so can be called externally
if (style == CREATE) {
double t_desired = atof(arg[2]);
int seed = atoi(arg[3]);
create(t_desired,seed);
}
else if (style == SET) set(narg-2,&arg[2]);
else if (style == SCALE) scale(narg-2,&arg[2]);
else if (style == RAMP) ramp(narg-2,&arg[2]);
else if (style == ZERO) zero(narg-2,&arg[2]);
}
/* ----------------------------------------------------------------------
initialization of defaults before calling velocity methods externaly
------------------------------------------------------------------------- */
void Velocity::init_external(const char *extgroup)
{
igroup = group->find(extgroup);
if (igroup == -1) error->all(FLERR,"Could not find velocity group ID");
groupbit = group->bitmask[igroup];
temperature = NULL;
dist_flag = 0;
sum_flag = 0;
momentum_flag = 1;
rotation_flag = 0;
loop_flag = ALL;
scale_flag = 1;
}
/* ---------------------------------------------------------------------- */
void Velocity::create(double t_desired, int seed)
{
int i;
if (seed <= 0) error->all(FLERR,"Illegal velocity create command");
// if temperature = NULL, create a new ComputeTemp with the velocity group
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning(FLERR,"Mismatch between velocity and compute groups");
temperature->init();
+ temperature->setup();
// store a copy of current velocities
double **v = atom->v;
int nlocal = atom->nlocal;
double **vhold;
memory->create(vhold,nlocal,3,"velocity:vnew");
for (i = 0; i < nlocal; i++) {
vhold[i][0] = v[i][0];
vhold[i][1] = v[i][1];
vhold[i][2] = v[i][2];
}
// create new velocities, in uniform or gaussian distribution
// loop option determines looping style, ALL is default
// ALL = loop over all natoms, only set those I own via atom->map
// cannot do this if atom IDs do not span 1-Natoms (some were deleted)
// will produce same V, independent of P, if atoms were read-in
// will NOT produce same V, independent of P, if used create_atoms
// LOCAL = only loop over my atoms, adjust RNG to be proc-specific
// will never produce same V, independent of P
// GEOM = only loop over my atoms
// choose RNG for each atom based on its xyz coord (geometry)
// via random->reset()
// will always produce same V, independent of P
// adjust by factor for atom mass
// for 2d, set Vz to 0.0
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int dimension = domain->dimension;
int m;
double vx,vy,vz,factor;
RanPark *random;
if (loop_flag == ALL) {
// create an atom map if one doesn't exist already
int mapflag = 0;
if (atom->map_style == 0) {
mapflag = 1;
atom->map_style = 1;
atom->nghost = 0;
atom->map_init();
atom->map_set();
}
// error check
if (atom->natoms > MAXSMALLINT)
error->all(FLERR,"Too big a problem to use velocity create loop all");
if (atom->tag_enable == 0)
error->all(FLERR,
"Cannot use velocity create loop all unless atoms have IDs");
if (atom->tag_consecutive() == 0)
error->all(FLERR,
"Atom IDs must be consecutive for velocity create loop all");
// loop over all atoms in system
// generate RNGs for all atoms, only assign to ones I own
// use either per-type mass or per-atom rmass
random = new RanPark(lmp,seed);
int natoms = static_cast<int> (atom->natoms);
for (i = 1; i <= natoms; i++) {
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
m = atom->map(i);
if (m >= 0 && m < nlocal) {
if (mask[m] & groupbit) {
if (rmass) factor = 1.0/sqrt(rmass[m]);
else factor = 1.0/sqrt(mass[type[m]]);
v[m][0] = vx * factor;
v[m][1] = vy * factor;
if (dimension == 3) v[m][2] = vz * factor;
else v[m][2] = 0.0;
}
}
}
// delete temporary atom map
if (mapflag) {
atom->map_delete();
atom->map_style = 0;
}
} else if (loop_flag == LOCAL) {
random = new RanPark(lmp,seed + comm->me);
for (i = 0; i < WARMUP; i++) random->uniform();
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
if (rmass) factor = 1.0/sqrt(rmass[i]);
else factor = 1.0/sqrt(mass[type[i]]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
if (dimension == 3) v[i][2] = vz * factor;
else v[i][2] = 0.0;
}
}
} else if (loop_flag == GEOM) {
random = new RanPark(lmp,1);
double **x = atom->x;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
random->reset(seed,x[i]);
if (dist_flag == 0) {
vx = random->uniform();
vy = random->uniform();
vz = random->uniform();
} else {
vx = random->gaussian();
vy = random->gaussian();
vz = random->gaussian();
}
if (rmass) factor = 1.0/sqrt(rmass[i]);
else factor = 1.0/sqrt(mass[type[i]]);
v[i][0] = vx * factor;
v[i][1] = vy * factor;
if (dimension == 3) v[i][2] = vz * factor;
else v[i][2] = 0.0;
}
}
}
// apply momentum and rotation zeroing
if (momentum_flag) zero_momentum();
if (rotation_flag) zero_rotation();
// scale temp to desired value
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if sum_flag set, add back in previous velocities
if (sum_flag) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] += vhold[i][0];
v[i][1] += vhold[i][1];
v[i][2] += vhold[i][2];
}
}
}
// free local memory
// if temperature was created, delete it
memory->destroy(vhold);
delete random;
if (tflag) delete temperature;
}
/* ---------------------------------------------------------------------- */
void Velocity::set(int narg, char **arg)
{
int xstyle,ystyle,zstyle,varflag;
double vx,vy,vz;
char *xstr,*ystr,*zstr;
int xvar,yvar,zvar;
// parse 3 args
xstyle = ystyle = zstyle = CONSTANT;
xstr = ystr = zstr = NULL;
if (strstr(arg[0],"v_") == arg[0]) {
int n = strlen(&arg[0][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[0][2]);
} else if (strcmp(arg[0],"NULL") == 0) xstyle = NONE;
else vx = atof(arg[0]);
if (strstr(arg[1],"v_") == arg[1]) {
int n = strlen(&arg[1][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[1][2]);
} else if (strcmp(arg[1],"NULL") == 0) ystyle = NONE;
else vy = atof(arg[1]);
if (strstr(arg[2],"v_") == arg[2]) {
int n = strlen(&arg[2][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[2][2]);
} else if (strcmp(arg[2],"NULL") == 0) zstyle = NONE;
else vz = atof(arg[2]);
// set and apply scale factors
xscale = yscale = zscale = 1.0;
if (xstyle && !xstr) {
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) xscale = domain->lattice->xlattice;
vx *= xscale;
}
if (ystyle && !ystr) {
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) yscale = domain->lattice->ylattice;
vy *= yscale;
}
if (zstyle && !zstr) {
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) zscale = domain->lattice->zlattice;
vz *= zscale;
}
// check variables
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for velocity set does not exist");
if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
else error->all(FLERR,"Variable for velocity set is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for velocity set does not exist");
if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
else error->all(FLERR,"Variable for velocity set is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for velocity set does not exist");
if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
else error->all(FLERR,"Variable for velocity set is invalid style");
}
if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else varflag = CONSTANT;
// error check for 2d models
if (domain->dimension == 2) {
if (zstyle == CONSTANT && vz != 0.0)
error->all(FLERR,"Cannot set non-zero z velocity for 2d simulation");
if (zstyle == EQUAL || zstyle == ATOM)
error->all(FLERR,"Cannot set variable z velocity for 2d simulation");
}
// allocate vfield array if necessary
double **vfield = NULL;
if (varflag == ATOM) memory->create(vfield,atom->nlocal,3,"velocity:vfield");
// set velocities via constants
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (sum_flag == 0) {
if (xstyle) v[i][0] = vx;
if (ystyle) v[i][1] = vy;
if (zstyle) v[i][2] = vz;
} else {
if (xstyle) v[i][0] += vx;
if (ystyle) v[i][1] += vy;
if (zstyle) v[i][2] += vz;
}
}
}
// set velocities via variables
} else {
if (xstyle == EQUAL) vx = input->variable->compute_equal(xvar);
else if (xstyle == ATOM && vfield)
input->variable->compute_atom(xvar,igroup,&vfield[0][0],3,0);
if (ystyle == EQUAL) vy = input->variable->compute_equal(yvar);
else if (ystyle == ATOM && vfield)
input->variable->compute_atom(yvar,igroup,&vfield[0][1],3,0);
if (zstyle == EQUAL) vz = input->variable->compute_equal(zvar);
else if (zstyle == ATOM && vfield)
input->variable->compute_atom(zvar,igroup,&vfield[0][2],3,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (sum_flag == 0) {
if (xstyle == ATOM) v[i][0] = vfield[i][0];
else if (xstyle) v[i][0] = vx;
if (ystyle == ATOM) v[i][1] = vfield[i][1];
else if (ystyle) v[i][1] = vy;
if (zstyle == ATOM) v[i][2] = vfield[i][2];
else if (zstyle) v[i][2] = vz;
} else {
if (xstyle == ATOM) v[i][0] += vfield[i][0];
else if (xstyle) v[i][0] += vx;
if (ystyle == ATOM) v[i][1] += vfield[i][1];
else if (ystyle) v[i][1] += vy;
if (zstyle == ATOM) v[i][2] += vfield[i][2];
else if (zstyle) v[i][2] += vz;
}
}
}
// clean up
delete [] xstr;
delete [] ystr;
delete [] zstr;
memory->destroy(vfield);
}
/* ----------------------------------------------------------------------
rescale velocities of a group after computing its temperature
------------------------------------------------------------------------- */
void Velocity::scale(int narg, char **arg)
{
double t_desired = atof(arg[0]);
// if temperature = NULL, create a new ComputeTemp with the velocity group
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
}
// initialize temperature computation
// warn if groups don't match
if (igroup != temperature->igroup && comm->me == 0)
error->warning(FLERR,"Mismatch between velocity and compute groups");
temperature->init();
+ temperature->setup();
// scale temp to desired value
double t = temperature->compute_scalar();
rescale(t,t_desired);
// if temperature was created, delete it
if (tflag) delete temperature;
}
/* ----------------------------------------------------------------------
apply a ramped set of velocities
------------------------------------------------------------------------- */
void Velocity::ramp(int narg, char **arg)
{
// set scale factors
if (scale_flag && domain->lattice == NULL)
error->all(FLERR,"Use of velocity with undefined lattice");
if (scale_flag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// parse args
int v_dim;
if (strcmp(arg[0],"vx") == 0) v_dim = 0;
else if (strcmp(arg[0],"vy") == 0) v_dim = 1;
else if (strcmp(arg[0],"vz") == 0) v_dim = 2;
else error->all(FLERR,"Illegal velocity command");
if (v_dim == 2 && domain->dimension == 2)
error->all(FLERR,"Velocity ramp in z for a 2d problem");
double v_lo,v_hi;
if (v_dim == 0) {
v_lo = xscale*atof(arg[1]);
v_hi = xscale*atof(arg[2]);
} else if (v_dim == 1) {
v_lo = yscale*atof(arg[1]);
v_hi = yscale*atof(arg[2]);
} else if (v_dim == 2) {
v_lo = zscale*atof(arg[1]);
v_hi = zscale*atof(arg[2]);
}
int coord_dim;
if (strcmp(arg[3],"x") == 0) coord_dim = 0;
else if (strcmp(arg[3],"y") == 0) coord_dim = 1;
else if (strcmp(arg[3],"z") == 0) coord_dim = 2;
else error->all(FLERR,"Illegal velocity command");
double coord_lo,coord_hi;
if (coord_dim == 0) {
coord_lo = xscale*atof(arg[4]);
coord_hi = xscale*atof(arg[5]);
} else if (coord_dim == 1) {
coord_lo = yscale*atof(arg[4]);
coord_hi = yscale*atof(arg[5]);
} else if (coord_dim == 2) {
coord_lo = zscale*atof(arg[4]);
coord_hi = zscale*atof(arg[5]);
}
// vramp = ramped velocity component for v_dim
// add or set based on sum_flag
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double fraction,vramp;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
fraction = (x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vramp = v_lo + fraction*(v_hi - v_lo);
if (sum_flag) v[i][v_dim] += vramp;
else v[i][v_dim] = vramp;
}
}
/* ----------------------------------------------------------------------
zero linear or angular momentum of a group
------------------------------------------------------------------------- */
void Velocity::zero(int narg, char **arg)
{
if (strcmp(arg[0],"linear") == 0) zero_momentum();
else if (strcmp(arg[0],"angular") == 0) zero_rotation();
else error->all(FLERR,"Illegal velocity command");
}
/* ----------------------------------------------------------------------
rescale velocities of group atoms to t_new from t_old
------------------------------------------------------------------------- */
void Velocity::rescale(double t_old, double t_new)
{
if (t_old == 0.0) error->all(FLERR,"Attempting to rescale a 0.0 temperature");
double factor = sqrt(t_new/t_old);
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
}
}
/* ----------------------------------------------------------------------
zero the linear momentum of a group of atoms by adjusting v by -Vcm
------------------------------------------------------------------------- */
void Velocity::zero_momentum()
{
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all(FLERR,"Cannot zero momentum of 0 atoms");
// compute velocity of center-of-mass of group
double masstotal = group->mass(igroup);
double vcm[3];
group->vcm(igroup,masstotal,vcm);
// adjust velocities by vcm to zero linear momentum
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vcm[0];
v[i][1] -= vcm[1];
v[i][2] -= vcm[2];
}
}
/* ----------------------------------------------------------------------
zero the angular momentum of a group of atoms by adjusting v by -(w x r)
------------------------------------------------------------------------- */
void Velocity::zero_rotation()
{
int i;
// cannot have 0 atoms in group
if (group->count(igroup) == 0)
error->all(FLERR,"Cannot zero momentum of 0 atoms");
// compute omega (angular velocity) of group around center-of-mass
double xcm[3],angmom[3],inertia[3][3],omega[3];
double masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,xcm);
group->angmom(igroup,xcm,angmom);
group->inertia(igroup,xcm,inertia);
group->omega(angmom,inertia,omega);
// adjust velocities to zero omega
// vnew_i = v_i - w x r_i
// must use unwrapped coords to compute r_i correctly
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
tagint *image = atom->image;
int nlocal = atom->nlocal;
double dx,dy,dz;
double unwrap[3];
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0]- xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
v[i][0] -= omega[1]*dz - omega[2]*dy;
v[i][1] -= omega[2]*dx - omega[0]*dz;
v[i][2] -= omega[0]*dy - omega[1]*dx;
}
}
/* ----------------------------------------------------------------------
parse optional parameters at end of velocity input line
------------------------------------------------------------------------- */
void Velocity::options(int narg, char **arg)
{
if (narg < 0) error->all(FLERR,"Illegal velocity command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"dist") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"uniform") == 0) dist_flag = 0;
else if (strcmp(arg[iarg+1],"gaussian") == 0) dist_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"sum") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) sum_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) sum_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"mom") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) momentum_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) momentum_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"rot") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"no") == 0) rotation_flag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) rotation_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
int icompute;
for (icompute = 0; icompute < modify->ncompute; icompute++)
if (strcmp(arg[iarg+1],modify->compute[icompute]->id) == 0) break;
if (icompute == modify->ncompute)
error->all(FLERR,"Could not find velocity temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Velocity temperature ID does not compute temperature");
iarg += 2;
} else if (strcmp(arg[iarg],"loop") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"all") == 0) loop_flag = ALL;
else if (strcmp(arg[iarg+1],"local") == 0) loop_flag = LOCAL;
else if (strcmp(arg[iarg+1],"geom") == 0) loop_flag = GEOM;
else error->all(FLERR,"Illegal velocity command");
iarg += 2;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal velocity command");
if (strcmp(arg[iarg+1],"box") == 0) scale_flag = 0;
else if (strcmp(arg[iarg+1],"lattice") == 0) scale_flag = 1;
else error->all(FLERR,"Illegal velocity command");
iarg += 2;
} else error->all(FLERR,"Illegal velocity command");
}
}