diff --git a/src/fix_temp_csvr.cpp b/src/fix_temp_csvr.cpp
index 81f87d4ca..3ef99ccd8 100644
--- a/src/fix_temp_csvr.cpp
+++ b/src/fix_temp_csvr.cpp
@@ -1,343 +1,344 @@
/* ----------------------------------------------------------------------
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 <string.h>
#include <stdlib.h>
#include <math.h>
#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);
} 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)
+ 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;
}
diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp
index 5e6036214..8af39df51 100644
--- a/src/fix_temp_rescale.cpp
+++ b/src/fix_temp_rescale.cpp
@@ -1,256 +1,257 @@
/* ----------------------------------------------------------------------
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 <string.h>
#include <stdlib.h>
#include <math.h>
#include "fix_temp_rescale.h"
#include "atom.h"
#include "force.h"
#include "group.h"
#include "update.h"
#include "domain.h"
#include "region.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
+ Fix(lmp, narg, arg),
+ tstr(NULL), id_temp(NULL), tflag(0)
{
if (narg < 8) error->all(FLERR,"Illegal fix temp/rescale command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix temp/rescale command");
scalar_flag = 1;
global_freq = nevery;
extscalar = 1;
tstr = NULL;
if (strstr(arg[4],"v_") == arg[4]) {
int n = strlen(&arg[4][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[4][2]);
tstyle = EQUAL;
} else {
t_start = force->numeric(FLERR,arg[4]);
t_target = t_start;
tstyle = CONSTANT;
}
t_stop = force->numeric(FLERR,arg[5]);
t_window = force->numeric(FLERR,arg[6]);
fraction = force->numeric(FLERR,arg[7]);
// create a new compute temp
// 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*[6];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
energy = 0.0;
}
/* ---------------------------------------------------------------------- */
FixTempRescale::~FixTempRescale()
{
delete [] tstr;
// delete temperature if fix created it
if (tflag) modify->delete_compute(id_temp);
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
int FixTempRescale::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTempRescale::init()
{
// check variable
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix temp/rescale does not exist");
if (input->variable->equalstyle(tvar)) tstyle = EQUAL;
else error->all(FLERR,"Variable for fix temp/rescale is invalid style");
}
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Temperature ID for fix temp/rescale does not exist");
temperature = modify->compute[icompute];
if (temperature->tempbias) which = BIAS;
else which = NOBIAS;
}
/* ---------------------------------------------------------------------- */
void FixTempRescale::end_of_step()
{
double t_current = temperature->compute_scalar();
// there is nothing to do, if there are no degrees of freedom
if (temperature->dof < 1) return;
// protect against division by zero.
if (t_current == 0.0)
error->all(FLERR,"Computed temperature for fix temp/rescale cannot be 0.0");
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
// set current t_target
// if variable temp, evaluate variable, wrap with clear/add
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/rescale variable returned negative temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
// rescale velocity of appropriate atoms if outside window
// for BIAS:
// temperature is current, so do not need to re-compute
// OK to not test returned v = 0, since factor is multiplied by v
if (fabs(t_current-t_target) > t_window) {
t_target = t_current - fraction*(t_current-t_target);
double factor = sqrt(t_target/t_current);
double efactor = 0.5 * force->boltz * temperature->dof;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
energy += (t_current-t_target) * efactor;
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
temperature->remove_bias(i,v[i]);
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
temperature->restore_bias(i,v[i]);
}
}
}
}
}
/* ---------------------------------------------------------------------- */
int FixTempRescale::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 FixTempRescale::reset_target(double t_new)
{
t_target = t_start = t_stop = t_new;
}
/* ---------------------------------------------------------------------- */
double FixTempRescale::compute_scalar()
{
return energy;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixTempRescale::extract(const char *str, int &dim)
{
if (strcmp(str,"t_target") == 0) {
dim = 0;
return &t_target;
}
return NULL;
}
diff --git a/src/fix_tmd.cpp b/src/fix_tmd.cpp
index d32668536..a94fbdcad 100644
--- a/src/fix_tmd.cpp
+++ b/src/fix_tmd.cpp
@@ -1,547 +1,546 @@
/* ----------------------------------------------------------------------
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 authors: Paul Crozier (SNL)
Christian Burisch (Bochum Univeristy, Germany)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_tmd.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "group.h"
#include "respa.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define CHUNK 1000
#define MAXLINE 256
/* ---------------------------------------------------------------------- */
-FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixTMD::FixTMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
+nfileevery(0), fp(NULL), xf(NULL), xold(NULL)
{
if (narg < 6) error->all(FLERR,"Illegal fix tmd command");
rho_stop = force->numeric(FLERR,arg[3]);
nfileevery = force->inumeric(FLERR,arg[5]);
if (rho_stop < 0 || nfileevery < 0)
error->all(FLERR,"Illegal fix tmd command");
if (nfileevery && narg != 7) error->all(FLERR,"Illegal fix tmd command");
MPI_Comm_rank(world,&me);
// perform initial allocation of atom-based arrays
// register with Atom class
- xf = NULL;
- xold = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
// make sure an atom map exists before reading in target coordinates
if (atom->map_style == 0)
error->all(FLERR,"Cannot use fix TMD unless atom map exists");
// read from arg[4] and store coordinates of final target in xf
readfile(arg[4]);
// open arg[6] statistics file and write header
if (nfileevery) {
if (narg != 7) error->all(FLERR,"Illegal fix tmd command");
if (me == 0) {
fp = fopen(arg[6],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix tmd file %s",arg[6]);
error->one(FLERR,str);
}
fprintf(fp,"%s %s\n","# Step rho_target rho_old gamma_back",
"gamma_forward lambda work_lambda work_analytical");
}
}
masstotal = group->mass(igroup);
if (masstotal == 0.0)
error->all(FLERR,"Cannot use fix TMD on massless group");
// rho_start = initial rho
// xold = initial x or 0.0 if not in group
int *mask = atom->mask;
int *type = atom->type;
imageint *image = atom->image;
double **x = atom->x;
double *mass = atom->mass;
int nlocal = atom->nlocal;
double dx,dy,dz;
rho_start = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],xold[i]);
dx = xold[i][0] - xf[i][0];
dy = xold[i][1] - xf[i][1];
dz = xold[i][2] - xf[i][2];
rho_start += mass[type[i]]*(dx*dx + dy*dy + dz*dz);
} else xold[i][0] = xold[i][1] = xold[i][2] = 0.0;
}
double rho_start_total;
MPI_Allreduce(&rho_start,&rho_start_total,1,MPI_DOUBLE,MPI_SUM,world);
rho_start = sqrt(rho_start_total/masstotal);
rho_old = rho_start;
work_lambda = 0.0;
work_analytical = 0.0;
previous_stat = 0;
}
/* ---------------------------------------------------------------------- */
FixTMD::~FixTMD()
{
if (nfileevery && me == 0) fclose(fp);
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
// delete locally stored arrays
memory->destroy(xf);
memory->destroy(xold);
}
/* ---------------------------------------------------------------------- */
int FixTMD::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTMD::init()
{
// check that no integrator fix comes after a TMD fix
int flag = 0;
for (int i = 0; i < modify->nfix; i++) {
if (strcmp(modify->fix[i]->style,"tmd") == 0) flag = 1;
if (flag && modify->fix[i]->time_integrate) flag = 2;
}
if (flag == 2) error->all(FLERR,"Fix tmd must come after integration fixes");
// timesteps
dtv = update->dt;
dtf = update->dt * force->ftm2v;
if (strstr(update->integrate_style,"respa"))
step_respa = ((Respa *) update->integrate)->step;
}
/* ---------------------------------------------------------------------- */
void FixTMD::initial_integrate(int vflag)
{
double a,b,c,d,e;
double dx,dy,dz,dxkt,dykt,dzkt;
double dxold,dyold,dzold,xback,yback,zback;
double gamma_forward,gamma_back,gamma_max,lambda;
double kt,fr,kttotal,frtotal,dtfm;
double unwrap[3];
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
imageint *image = atom->image;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delta = update->ntimestep - update->beginstep;
if (delta != 0.0) delta /= update->endstep - update->beginstep;
double rho_target = rho_start + delta * (rho_stop - rho_start);
// compute the Lagrange multiplier
a = b = e = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dxold = xold[i][0] - xf[i][0];
dyold = xold[i][1] - xf[i][1];
dzold = xold[i][2] - xf[i][2];
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xf[i][0];
dy = unwrap[1] - xf[i][1];
dz = unwrap[2] - xf[i][2];
a += mass[type[i]]*(dxold*dxold + dyold*dyold + dzold*dzold);
b += mass[type[i]]*(dx *dxold + dy *dyold + dz *dzold);
e += mass[type[i]]*(dx *dx + dy *dy + dz *dz);
}
}
double abe[3],abetotal[3];
abe[0] = a; abe[1] = b; abe[2] = e;
MPI_Allreduce(abe,abetotal,3,MPI_DOUBLE,MPI_SUM,world);
a = abetotal[0]/masstotal;
b = 2.0*abetotal[1]/masstotal;
e = abetotal[2]/masstotal;
c = e - rho_old*rho_old;
d = b*b - 4*a*c;
if (d < 0) d = 0;
if (b >= 0) gamma_max = (-b - sqrt(d))/(2*a);
else gamma_max = (-b + sqrt(d))/(2*a);
gamma_back = c/(a*gamma_max);
if (a == 0.0) gamma_back = 0;
c = e - rho_target*rho_target;
d = b*b - 4*a*c;
if (d < 0) d = 0;
if (b >= 0) gamma_max = (-b - sqrt(d))/(2*a);
else gamma_max = (-b + sqrt(d))/(2*a);
gamma_forward = c/(a*gamma_max);
if (a == 0.0) gamma_forward = 0;
fr = kt = 0.0;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dxold = xold[i][0] - xf[i][0];
dyold = xold[i][1] - xf[i][1];
dzold = xold[i][2] - xf[i][2];
domain->unmap(x[i],image[i],unwrap);
xback = unwrap[0] + gamma_back*dxold;
yback = unwrap[1] + gamma_back*dyold;
zback = unwrap[2] + gamma_back*dzold;
dxkt = xback - xold[i][0];
dykt = yback - xold[i][1];
dzkt = zback - xold[i][2];
kt += mass[type[i]]*(dxkt*dxkt + dykt*dykt + dzkt*dzkt);
fr += f[i][0]*dxold + f[i][1]*dyold + f[i][2]*dzold;
}
}
double r[2],rtotal[2];
r[0] = fr; r[1] = kt;
MPI_Allreduce(r,rtotal,2,MPI_DOUBLE,MPI_SUM,world);
frtotal = rtotal[0];
kttotal = rtotal[1];
// stat write of mean constraint force based on previous time step constraint
if (nfileevery && me == 0) {
work_analytical +=
(-frtotal - kttotal/dtv/dtf)*(rho_target - rho_old)/rho_old;
lambda = gamma_back*rho_old*masstotal/dtv/dtf;
work_lambda += lambda*(rho_target - rho_old);
if (!(update->ntimestep % nfileevery) &&
(previous_stat != update->ntimestep)) {
fprintf(fp,
BIGINT_FORMAT " %g %g %g %g %g %g %g\n",
update->ntimestep,rho_target,rho_old,
gamma_back,gamma_forward,lambda,work_lambda,work_analytical);
fflush(fp);
previous_stat = update->ntimestep;
}
}
rho_old = rho_target;
// apply the constraint and save constrained positions for next step
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
dxold = xold[i][0] - xf[i][0];
x[i][0] += gamma_forward*dxold;
v[i][0] += gamma_forward*dxold/dtv;
f[i][0] += gamma_forward*dxold/dtv/dtfm;
dyold = xold[i][1] - xf[i][1];
x[i][1] += gamma_forward*dyold;
v[i][1] += gamma_forward*dyold/dtv;
f[i][1] += gamma_forward*dyold/dtv/dtfm;
dzold = xold[i][2] - xf[i][2];
x[i][2] += gamma_forward*dzold;
v[i][2] += gamma_forward*dzold/dtv;
f[i][2] += gamma_forward*dzold/dtv/dtfm;
domain->unmap(x[i],image[i],xold[i]);
}
}
}
/* ---------------------------------------------------------------------- */
void FixTMD::initial_integrate_respa(int vflag, int ilevel, int flag)
{
if (flag) return; // only used by NPT,NPH
dtv = step_respa[ilevel];
dtf = step_respa[ilevel] * force->ftm2v;
if (ilevel == 0) initial_integrate(vflag);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixTMD::memory_usage()
{
double bytes = 2*atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based arrays
------------------------------------------------------------------------- */
void FixTMD::grow_arrays(int nmax)
{
memory->grow(xf,nmax,3,"fix_tmd:xf");
memory->grow(xold,nmax,3,"fix_tmd:xold");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixTMD::copy_arrays(int i, int j, int delflag)
{
xf[j][0] = xf[i][0];
xf[j][1] = xf[i][1];
xf[j][2] = xf[i][2];
xold[j][0] = xold[i][0];
xold[j][1] = xold[i][1];
xold[j][2] = xold[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixTMD::pack_exchange(int i, double *buf)
{
buf[0] = xf[i][0];
buf[1] = xf[i][1];
buf[2] = xf[i][2];
buf[3] = xold[i][0];
buf[4] = xold[i][1];
buf[5] = xold[i][2];
return 6;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixTMD::unpack_exchange(int nlocal, double *buf)
{
xf[nlocal][0] = buf[0];
xf[nlocal][1] = buf[1];
xf[nlocal][2] = buf[2];
xold[nlocal][0] = buf[3];
xold[nlocal][1] = buf[4];
xold[nlocal][2] = buf[5];
return 6;
}
/* ----------------------------------------------------------------------
read target coordinates from file, store with appropriate atom
------------------------------------------------------------------------- */
void FixTMD::readfile(char *file)
{
if (me == 0) {
if (screen) fprintf(screen,"Reading TMD target file %s ...\n",file);
open(file);
}
int *mask = atom->mask;
int nlocal = atom->nlocal;
char *buffer = new char[CHUNK*MAXLINE];
char *next,*bufptr;
int i,m,nlines,imageflag,ix,iy,iz;
tagint itag;
double x,y,z,xprd,yprd,zprd;
int firstline = 1;
int ncount = 0;
char *eof = NULL;
xprd = yprd = zprd = -1.0;
while (!eof) {
if (me == 0) {
m = 0;
for (nlines = 0; nlines < CHUNK; nlines++) {
eof = fgets(&buffer[m],MAXLINE,fp);
if (eof == NULL) break;
m += strlen(&buffer[m]);
}
if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
m++;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
MPI_Bcast(&nlines,1,MPI_INT,0,world);
MPI_Bcast(&m,1,MPI_INT,0,world);
MPI_Bcast(buffer,m,MPI_CHAR,0,world);
bufptr = buffer;
for (i = 0; i < nlines; i++) {
next = strchr(bufptr,'\n');
*next = '\0';
if (firstline) {
if (strstr(bufptr,"xlo xhi")) {
double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi);
xprd = hi - lo;
bufptr = next + 1;
continue;
} else if (strstr(bufptr,"ylo yhi")) {
double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi);
yprd = hi - lo;
bufptr = next + 1;
continue;
} else if (strstr(bufptr,"zlo zhi")) {
double lo,hi;
sscanf(bufptr,"%lg %lg",&lo,&hi);
zprd = hi - lo;
bufptr = next + 1;
continue;
} else if (atom->count_words(bufptr) == 4) {
if (xprd >= 0.0 || yprd >= 0.0 || zprd >= 0.0)
error->all(FLERR,"Incorrect format in TMD target file");
imageflag = 0;
firstline = 0;
} else if (atom->count_words(bufptr) == 7) {
if (xprd < 0.0 || yprd < 0.0 || zprd < 0.0)
error->all(FLERR,"Incorrect format in TMD target file");
imageflag = 1;
firstline = 0;
} else error->all(FLERR,"Incorrect format in TMD target file");
}
if (imageflag)
sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d",
&itag,&x,&y,&z,&ix,&iy,&iz);
else
sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z);
m = atom->map(itag);
if (m >= 0 && m < nlocal && mask[m] & groupbit) {
if (imageflag) {
xf[m][0] = x + ix*xprd;
xf[m][1] = y + iy*yprd;
xf[m][2] = z + iz*zprd;
} else {
xf[m][0] = x;
xf[m][1] = y;
xf[m][2] = z;
}
ncount++;
}
bufptr = next + 1;
}
}
// clean up
delete [] buffer;
if (me == 0) {
if (compressed) pclose(fp);
else fclose(fp);
}
// check that all atoms in group were listed in target file
// set xf = 0.0 for atoms not in group
int gcount = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) gcount++;
else xf[i][0] = xf[i][1] = xf[i][2] = 0.0;
int flag = 0;
if (gcount != ncount) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"TMD target file did not list all group atoms");
}
/* ----------------------------------------------------------------------
proc 0 opens TMD data file
test if gzipped
------------------------------------------------------------------------- */
void FixTMD::open(char *file)
{
compressed = 0;
char *suffix = file + strlen(file) - 3;
if (suffix > file && strcmp(suffix,".gz") == 0) compressed = 1;
if (!compressed) fp = fopen(file,"r");
else {
#ifdef LAMMPS_GZIP
char gunzip[128];
sprintf(gunzip,"gzip -c -d %s",file);
#ifdef _WIN32
fp = _popen(gunzip,"rb");
#else
fp = popen(gunzip,"r");
#endif
#else
error->one(FLERR,"Cannot open gzipped file");
#endif
}
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(FLERR,str);
}
}
/* ---------------------------------------------------------------------- */
void FixTMD::reset_dt()
{
dtv = update->dt;
dtf = update->dt * force->ftm2v;
}
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
index d4bd3087d..07841d5ba 100644
--- a/src/fix_vector.cpp
+++ b/src/fix_vector.cpp
@@ -1,337 +1,339 @@
/* ----------------------------------------------------------------------
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 <string.h>
#include "fix_vector.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING,WINDOW};
enum{SCALAR,VECTOR};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
/* ---------------------------------------------------------------------- */
FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
+ Fix(lmp, narg, arg),
+ nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL), vector(NULL), array(NULL)
{
if (narg < 5) error->all(FLERR,"Illegal fix vector command");
nevery = force->inumeric(FLERR,arg[3]);
if (nevery <= 0) error->all(FLERR,"Illegal fix vector command");
nvalues = narg-4;
which = new int[nvalues];
argindex = new int[nvalues];
value2index = new int[nvalues];
ids = new char*[nvalues];
nvalues = 0;
for (int iarg = 4; iarg < narg; iarg++) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
else error->all(FLERR,"Illegal fix vector command");
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix vector command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
nvalues++;
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix vector does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all(FLERR,"Fix vector compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all(FLERR,"Fix vector compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all(FLERR,
"Fix vector compute vector is accessed out-of-range");
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix vector does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all(FLERR,"Fix vector fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all(FLERR,"Fix vector fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all(FLERR,"Fix vector fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all(FLERR,
"Fix for fix vector not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix vector does not exist");
if (argindex[i] == 0 && input->variable->equalstyle(ivariable) == 0)
error->all(FLERR,"Fix vector variable is not equal-style variable");
if (argindex[i] && input->variable->vectorstyle(ivariable) == 0)
error->all(FLERR,"Fix vector variable is not vector-style variable");
}
}
// this fix produces either a global vector or array
// intensive/extensive flags set by compute,fix,variable that produces value
int value,finalvalue;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[i])];
if (argindex[0] == 0) value = compute->extscalar;
else if (compute->extvector >= 0) value = compute->extvector;
else value = compute->extlist[argindex[0]-1];
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[i])];
if (argindex[i] == 0) value = fix->extvector;
else value = fix->extarray;
} else if (which[i] == VARIABLE) value = 0;
if (i == 0) finalvalue = value;
else if (value != finalvalue)
error->all(FLERR,"Fix vector cannot set output array "
"intensive/extensive from these inputs");
}
if (nvalues == 1) {
vector_flag = 1;
extvector = finalvalue;
} else {
array_flag = 1;
size_array_cols = nvalues;
extarray = finalvalue;
}
global_freq = nevery;
time_depend = 1;
// ncount = current size of vector or array
vector = NULL;
array = NULL;
ncount = ncountmax = 0;
if (nvalues == 1) size_vector = 0;
else size_array_rows = 0;
// nextstep = next step on which end_of_step does something
// add nextstep to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nextstep = (update->ntimestep/nevery)*nevery;
if (nextstep < update->ntimestep) nextstep += nevery;
modify->addstep_compute_all(nextstep);
// initialstep = first step the vector/array will store values for
initialstep = nextstep;
}
/* ---------------------------------------------------------------------- */
FixVector::~FixVector()
{
delete [] which;
delete [] argindex;
delete [] value2index;
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
memory->destroy(vector);
memory->destroy(array);
}
/* ---------------------------------------------------------------------- */
int FixVector::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixVector::init()
{
// set current indices for all computes,fixes,variables
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix vector does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix vector does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix vector does not exist");
value2index[i] = ivariable;
}
}
// reallocate vector or array for accumulated size at end of run
// use endstep to allow for subsequent runs with "pre no"
// nsize = # of entries from initialstep to finalstep
bigint finalstep = update->endstep/nevery * nevery;
if (finalstep > update->endstep) finalstep -= nevery;
ncountmax = (finalstep-initialstep)/nevery + 1;
if (nvalues == 1) memory->grow(vector,ncountmax,"vector:vector");
else memory->grow(array,ncountmax,nvalues,"vector:array");
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixVector::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixVector::end_of_step()
{
// skip if not step which requires doing something
if (update->ntimestep != nextstep) return;
if (ncount == ncountmax)
error->all(FLERR,"Overflow of allocated fix vector storage");
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
double *result;
if (nvalues == 1) result = &vector[ncount];
else result = array[ncount];
modify->clearstep_compute();
for (int i = 0; i < nvalues; i++) {
int m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
result[i] = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
result[i] = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
result[i] = modify->fix[m]->compute_scalar();
else
result[i] = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style or vector-style variable
- } else if (which[i] == VARIABLE)
- if (argindex[i] == 0)
+ } else if (which[i] == VARIABLE) {
+ if (argindex[i] == 0)
result[i] = input->variable->compute_equal(m);
else {
double *varvec;
int nvec = input->variable->compute_vector(m,&varvec);
int index = argindex[i];
if (nvec < index) result[i] = 0.0;
else result[i] = varvec[index-1];
}
+ }
}
// trigger computes on next needed step
nextstep += nevery;
modify->addstep_compute(nextstep);
// update size of vector or array
ncount++;
if (nvalues == 1) size_vector++;
else size_array_rows++;
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixVector::compute_vector(int i)
{
return vector[i];
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixVector::compute_array(int i, int j)
{
return array[i][j];
}
diff --git a/src/fix_viscous.cpp b/src/fix_viscous.cpp
index 9c82b34d8..911fcf84e 100644
--- a/src/fix_viscous.cpp
+++ b/src/fix_viscous.cpp
@@ -1,144 +1,145 @@
/* ----------------------------------------------------------------------
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 <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_viscous.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixViscous::FixViscous(LAMMPS *lmp, int narg, char **arg) :
- Fix(lmp, narg, arg)
+ Fix(lmp, narg, arg),
+ gamma(NULL)
{
if (narg < 4) error->all(FLERR,"Illegal fix viscous command");
double gamma_one = force->numeric(FLERR,arg[3]);
gamma = new double[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) gamma[i] = gamma_one;
// optional args
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix viscous command");
int itype = force->inumeric(FLERR,arg[iarg+1]);
double scale = force->numeric(FLERR,arg[iarg+2]);
if (itype <= 0 || itype > atom->ntypes)
error->all(FLERR,"Illegal fix viscous command");
gamma[itype] = gamma_one * scale;
iarg += 3;
} else error->all(FLERR,"Illegal fix viscous command");
}
respa_level_support = 1;
ilevel_respa = 0;
}
/* ---------------------------------------------------------------------- */
FixViscous::~FixViscous()
{
delete [] gamma;
}
/* ---------------------------------------------------------------------- */
int FixViscous::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixViscous::init()
{
int max_respa = 0;
if (strstr(update->integrate_style,"respa")) {
ilevel_respa = max_respa = ((Respa *) update->integrate)->nlevels-1;
if (respa_level >= 0) ilevel_respa = MIN(respa_level,max_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixViscous::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
post_force_respa(vflag,ilevel_respa,0);
((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
}
}
/* ---------------------------------------------------------------------- */
void FixViscous::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixViscous::post_force(int vflag)
{
// apply drag force to atoms in group
// direction is opposed to velocity vector
// magnitude depends on atom type
double **v = atom->v;
double **f = atom->f;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double drag;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
drag = gamma[type[i]];
f[i][0] -= drag*v[i][0];
f[i][1] -= drag*v[i][1];
f[i][2] -= drag*v[i][2];
}
}
/* ---------------------------------------------------------------------- */
void FixViscous::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == ilevel_respa) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixViscous::min_post_force(int vflag)
{
post_force(vflag);
}