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fix_qbmsst.cpp
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fix_qbmsst.cpp
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/* ----------------------------------------------------------------------
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: Shen,Yuan, Qi,Tingting, and Reed,Evan
Implementation of the Multi-Scale Shock Method with quantum nuclear effects
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_qbmsst.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "input.h"
#include "output.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "group.h"
#include "kspace.h"
#include "thermo.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ----------------------------------------------------------------------
read parameters
------------------------------------------------------------------------- */
FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 5) error->all(FLERR,"Illegal fix qbmsst command");
if ( strcmp(arg[3],"x") == 0 )
direction = 0;
else if ( strcmp(arg[3],"y") == 0 )
direction = 1;
else if ( strcmp(arg[3],"z") == 0 )
direction = 2;
else {
error->all(FLERR,"Illegal fix qbmsst command");
}
velocity = atof(arg[4]);
if ( velocity < 0 )
error->all(FLERR,"Illegal fix qbmsst command");
// default parameters
global_freq = 1;
extscalar = 1;
extvector = 0;
nevery = 1;
restart_global = 1;
box_change_size = 1;
time_integrate = 1;
scalar_flag = 1;
vector_flag = 1;
size_vector = 5;
qmass = 1.0e1;
mu = 0.0;
p0 = 0.0;
v0 = 1.0;
e0 = 0.0;
p0_set = 0;
v0_set = 0;
e0_set = 0;
tscale = 0.01;
t_period = 1.0;
fric_coef = 1/t_period;
seed = 880302;
f_max = 200.0;
N_f = 100;
eta = 1.0;
beta = 100;
t_init = 300.0;
qtb_set = 0;
// reading parameters
int iarg = 5;
while (iarg < narg) {
if (strcmp(arg[iarg],"q") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
qmass = atof(arg[iarg+1]); if (qmass < 0.0) error->all(FLERR,"Fix qbmsst qmass must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"mu") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
mu = atof(arg[iarg+1]); if (mu < 0.0) error->all(FLERR,"Fix qbmsst mu must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"p0") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
p0 = atof(arg[iarg+1]); if (p0 < 0.0) error->all(FLERR,"Fix qbmsst p0 must be >= 0.0");
p0_set = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"v0") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
v0 = atof(arg[iarg+1]); if (v0 < 0.0) error->all(FLERR,"Fix qbmsst v0 must be >= 0.0");
v0_set = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"e0") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
e0 = atof(arg[iarg+1]);
e0_set = 1;
iarg += 2;
} else if (strcmp(arg[iarg],"tscale") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
tscale = atof(arg[iarg+1]); if (tscale < 0.0 || tscale > 1.0) error->all(FLERR,"Fix qbmsst tscale must satisfy 0 <= tscale < 1");
iarg += 2;
} else if (strcmp(arg[iarg],"damp") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
t_period = atof(arg[iarg+1]); if (t_period <= 0.0) error->all(FLERR,"Fix qbmsst damp must be > 0.0"); fric_coef = 1/t_period;
iarg += 2;
} else if (strcmp(arg[iarg],"seed") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
seed = atof(arg[iarg+1]); if (seed <= 0) error->all(FLERR,"Fix qbmsst seed must be a positive integer");
iarg += 2;
} else if (strcmp(arg[iarg],"f_max") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
f_max = atof(arg[iarg+1]); if (f_max <= 0) error->all(FLERR,"Fix qbmsst f_max must be > 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"N_f") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
N_f = atof(arg[iarg+1]); if (N_f <= 0) error->all(FLERR,"Fix qbmsst N_f must be a positive integer");
iarg += 2;
} else if (strcmp(arg[iarg],"eta") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
eta = atof(arg[iarg+1]); if (eta <= 0) error->all(FLERR,"Fix qbmsst eta must be >= 0.0");
iarg += 2;
} else if (strcmp(arg[iarg],"beta") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
beta = atof(arg[iarg+1]); if (beta <= 0) error->all(FLERR,"Fix qbmsst beta must be a positive integer");
iarg += 2;
} else if (strcmp(arg[iarg],"T_init") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix qbmsst command");
t_init = atof(arg[iarg+1]); if (t_init <= 0) error->all(FLERR,"Fix qbmsst T_init must be >= 0.0");
iarg += 2;
} else error->all(FLERR,"Illegal fix qbmsst command");
}
// check for periodicity in controlled dimensions
if (domain->nonperiodic) error->all(FLERR,"Fix qbmsst requires a periodic box");
// comments
if (comm->me == 0) {
if (screen) {
fprintf(screen,"QBMSST parameters:\n");
if (direction == 0) fprintf(screen," Shock in x direction\n");
else if (direction == 1) fprintf(screen," Shock in y direction\n");
else if (direction == 2) fprintf(screen," Shock in z direction\n");
fprintf(screen," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(screen," Shock velocity = %12.5e\n", velocity);
fprintf(screen," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
if (p0_set)
fprintf(screen," Initial pressure specified to be %12.5e\n", p0);
else fprintf(screen," Initial pressure calculated on first step\n");
if (v0_set)
fprintf(screen," Initial volume specified to be %12.5e\n", v0);
else fprintf(screen," Initial volume calculated on first step\n");
if (e0_set)
fprintf(screen," Initial energy specified to be %12.5e\n", e0);
else fprintf(screen," Initial energy calculated on first step\n");
}
if (logfile) {
fprintf(logfile,"QBMSST parameters:\n");
if (direction == 0) fprintf(logfile," Shock in x direction\n");
else if (direction == 1) fprintf(logfile," Shock in y direction\n");
else if (direction == 2) fprintf(logfile," Shock in z direction\n");
fprintf(logfile," Cell mass-like parameter qmass (units of mass^2/length^4) = %12.5e\n", qmass);
fprintf(logfile," Shock velocity = %12.5e\n", velocity);
fprintf(logfile," Artificial viscosity (units of mass/length/time) = %12.5e\n", mu);
if (p0_set)
fprintf(logfile," Initial pressure specified to be %12.5e\n", p0);
else fprintf(logfile," Initial pressure calculated on first step\n");
if (v0_set)
fprintf(logfile," Initial volume specified to be %12.5e\n", v0);
else fprintf(logfile," Initial volume calculated on first step\n");
if (e0_set)
fprintf(logfile," Initial energy specified to be %12.5e\n", e0);
else fprintf(logfile," Initial energy calculated on first step\n");
}
}
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
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] = const_cast<char *>("all");
newarg[2] = const_cast<char *>("temp");
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = const_cast<char *>("all");
newarg[2] = const_cast<char *>("pressure");
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pflag = 1;
// create a new compute potential energy compute
n = strlen(id) + 3;
id_pe = new char[n];
strcpy(id_pe,id);
strcat(id_pe,"_pe");
newarg = new char*[3];
newarg[0] = id_pe;
newarg[1] = (char*)"all";
newarg[2] = (char*)"pe";
modify->add_compute(3,newarg);
delete [] newarg;
peflag = 1;
// allocate qbmsst
temperature = NULL;
pressure = NULL;
pe = NULL;
old_velocity = NULL;
rfix = NULL;
gfactor = NULL;
random = NULL;
omega_H = NULL;
time_H = NULL;
random_array_0 = NULL;
random_array_1 = NULL;
random_array_2 = NULL;
fran = NULL;
// initialize Marsagxlia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// allocate per-type arrays for force prefactors
gfactor = new double[atom->ntypes+1];
// allocate random-arrays and fran
grow_arrays(atom->nmax);
atom->add_callback(0);
// allocate omega_H and time_H
memory->create(omega_H,2*N_f,"qbmsst:omega_H");
memory->create(time_H,2*N_f,"qbmsst:time_H");
// initiate velocity record array
memory->create(old_velocity,atom->nlocal,3,"qbmsst:old_velocity");
atoms_allocated = atom->nlocal;
}
/* ----------------------------------------------------------------------
release memories
------------------------------------------------------------------------- */
FixQBMSST::~FixQBMSST()
{
delete [] rfix;
delete [] gfactor;
delete random;
// delete temperature and pressure if fix created them
if (tflag) modify->delete_compute(id_temp);
if (pflag) modify->delete_compute(id_press);
if (peflag) modify->delete_compute(id_pe);
delete [] id_temp;
delete [] id_press;
delete [] id_pe;
memory->destroy(old_velocity);
memory->destroy(fran);
memory->destroy(random_array_0);
memory->destroy(random_array_1);
memory->destroy(random_array_2);
memory->destroy(omega_H);
memory->destroy(time_H);
atom->delete_callback(id,0);
}
/* ----------------------------------------------------------------------
setmask
------------------------------------------------------------------------- */
int FixQBMSST::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= THERMO_ENERGY;
return mask;
}
/* ----------------------------------------------------------------------
fix initiation
------------------------------------------------------------------------- */
void FixQBMSST::init()
{
// copy parameters from other classes
dtv = update->dt;
dthalf = 0.5 * update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
ntotal = atom->natoms;
boltz = force->boltz;
nktv2p = force->nktv2p;
mvv2e = force->mvv2e;
if (atom->mass == NULL)
error->all(FLERR,"Cannot use fix qbmsst without per-type mass defined");
// set compute ptrs
int itemp = modify->find_compute(id_temp);
int ipress = modify->find_compute(id_press);
int ipe = modify->find_compute(id_pe);
if (itemp < 0 || ipress < 0|| ipe < 0)
error->all(FLERR,"Could not find fix qbmsst compute ID");
if (modify->compute[itemp]->tempflag == 0)
error->all(FLERR,"Fix qbmsst compute ID does not compute temperature");
if (modify->compute[ipress]->pressflag == 0)
error->all(FLERR,"Fix qbmsst compute ID does not compute pressure");
if (modify->compute[ipe]->peflag == 0)
error->all(FLERR,"Fix qbmsst compute ID does not compute potential energy");
temperature = modify->compute[itemp];
pressure = modify->compute[ipress];
pe = modify->compute[ipe];
// initiate the counter l and \mu
counter_l=0;
counter_mu=0;
// initiate qtb temperature
if (!qtb_set) {
t_current = t_init; qtb_set=1;
}
old_eavg = e0;
//set up the h time step for updating the random force \delta{}h=\frac{\pi}{\Omega_{max}}
if (int(1.0/(2*f_max*dtv)) == 0) {
if (comm->me == 0) printf ("Warning: Either f_max is too high or the time step is too big, setting f_max to be 1/timestep!\n");
h_timestep=dtv;
alpha=1;
} else {
alpha=int(1.0/(2*f_max*dtv));
h_timestep=alpha*dtv;
}
if (comm->me == 0) printf ("The effective maximum frequncy is now %f inverse time unit with alpha value as %d!\n", 0.5/h_timestep, alpha);
//gfactor is the random force \sqrt{\frac{2\gamma{}m_{i}}{\alpha*\delta{}t}}, \sqrt{12} makes the random array variance equal to unit.
for (int i = 1; i <= atom->ntypes; i++) {
gfactor[i] = sqrt(2*fric_coef*atom->mass[i])*sqrt(force->mvv2e)*sqrt(12/h_timestep);//this still leaves a square energy term from the power spectrum H.
}
// generate random number array with zero mean and variance equal 1/12.
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
for (int m = 0; m < 2*N_f; m++) {
random_array_0[i][m] = random->uniform()-0.5;
random_array_1[i][m] = random->uniform()-0.5;
random_array_2[i][m] = random->uniform()-0.5;
}
}
// initiate dilations
dilation[0] = dilation[1] = dilation[2] = 1.0;
// initialize the time derivative of the volume.
omega[0] = omega[1] = omega[2] = 0.0;
// compute total mass
double mass = 0.0;
for (int i = 0; i < atom->nlocal; i++) mass += atom->mass[atom->type[i]];
MPI_Allreduce(&mass,&total_mass,1,MPI_DOUBLE,MPI_SUM,world);
// enable kspace summation of long range forces
if (force->kspace) kspace_flag = 1;
else kspace_flag = 0;
// detect if any fix rigid exist so rigid bodies move when box is dilated
// rfix[] = indices to each fix rigid
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
strcmp(modify->fix[i]->style,"poems") == 0) nrigid++;
if (nrigid) {
rfix = new int[nrigid];
nrigid = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0 ||
strcmp(modify->fix[i]->style,"poems") == 0) rfix[nrigid++] = i;
}
}
/* ----------------------------------------------------------------------
compute T,P before integrator starts
------------------------------------------------------------------------- */
void FixQBMSST::setup(int vflag)
{
lagrangian_position = 0.0;
temperature->compute_vector();
pressure->compute_vector();
couple();
velocity_sum = compute_vsum();
if ( v0_set == 0 ) {
v0 = compute_vol();
v0_set = 1;
if (comm->me == 0) {
if ( screen ) fprintf(screen,"Fix QBMSST v0 = %12.5e\n", v0);
if ( logfile ) fprintf(logfile,"Fix QBMSST v0 = %12.5e\n", v0);
}
}
if ( p0_set == 0 ) {
p0 = p_current[direction];
p0_set = 1;
if ( comm->me == 0 ) {
if ( screen ) fprintf(screen,"Fix QBMSST p0 = %12.5e\n", p0);
if ( logfile ) fprintf(logfile,"Fix QBMSST p0 = %12.5e\n", p0);
}
}
if ( e0_set == 0 ) {
e0 = compute_etotal();
e0_set = 1;
old_eavg = e0;
if ( comm->me == 0 ) {
if ( screen ) fprintf(screen,"Fix QBMSST e0 = to be %12.5e\n",e0);
if ( logfile ) fprintf(logfile,"Fix QBMSST e0 = to be %12.5e\n",e0);
}
}
temperature->compute_vector();
double *ke_tensor = temperature->vector;
double ke_temp = ke_tensor[0]+ke_tensor[1]+ke_tensor[2];
if (ke_temp > 0.0 && tscale > 0.0 ) {
// transfer energy from atom velocities to cell volume motion
// to bias initial compression
double **v = atom->v;
int *mask = atom->mask;
double sqrt_initial_temperature_scaling = sqrt(1.0-tscale);
double fac1 = tscale*total_mass/qmass*ke_temp/force->mvv2e;
omega[direction]=-1*sqrt(fac1);
double fac2 = omega[direction]/v0;
if ( comm->me == 0 && tscale != 1.0) {
if ( screen )
fprintf(screen,"Fix QBMSST initial strain rate of %12.5e established "
"by reducing temperature by factor of %12.5e\n",
fac2,tscale);
if ( logfile )
fprintf(logfile,"Fix QBMSST initial strain rate of %12.5e established "
"by reducing temperature by factor of %12.5e\n",
fac2,tscale);
}
for (int i = 0; i < atom->nlocal; i++) {
if (mask[i] & groupbit) {
for (int k = 0; k < 3; k++ ) {
v[i][k]*=sqrt_initial_temperature_scaling;
}
}
}
}
// trigger virial computation on next timestep
pressure->addstep(update->ntimestep+1);
pe->addstep(update->ntimestep+1);
}
/* ----------------------------------------------------------------------
1st half of Verlet update
------------------------------------------------------------------------- */
void FixQBMSST::initial_integrate(int vflag)
{
int sd;
sd = direction;
double p_qbmsst;// QBMSST driving pressure.
int i, k;
double vol;
int nlocal = atom->nlocal;
int *mask = atom->mask;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
double **x = atom->x;
double boltz = force->boltz;
// check to see if old_velocity is correctly allocated
check_alloc(nlocal);
// compute new pressure and volume.
temperature->compute_vector();
pressure->compute_vector();
couple();
vol = compute_vol();
// decide if the qtb temperature need to be updated or not
if (counter_l == 0) {
t_current -= dtv*fric_coef*eta*beta*(old_eavg-e0)/(3*ntotal*boltz);
old_eavg = 0;//clear old energy average
if (t_current < 0.0) t_current=0;
// load omega_H with calculated spectrum at a specific temperature (corrected spectrum), omega_H is the Fourier transformation of time_H
for (int k = 0; k < 2*N_f; k++) {
double f_k=(k-N_f)/(2*N_f*h_timestep); //\omega_k=\frac{2\pi}{\delta{}h}\frac{k}{2N_f} for k from -N_f to N_f-1
if(k == N_f) {
omega_H[k]=sqrt(force->boltz * t_current);
} else {
double energy_k= force->hplanck * fabs(f_k);
omega_H[k]=sqrt( energy_k * (0.5+1.0/( exp(energy_k/(force->boltz * t_current)) - 1.0 )) );
omega_H[k]*=alpha*sin((k-N_f)*M_PI/(2*alpha*N_f))/sin((k-N_f)*M_PI/(2*N_f));
}
}
// construct the signal filter H, filter has the unit of of sqrt(energy) \sqrt{2N_f}^{-1}H\left(t_n\right)
for (int n = 0; n < 2*N_f; n++) {
time_H[n] = 0;
double t_n=(n-N_f);
for (int k = 0; k < 2*N_f; k++) {
double omega_k=(k-N_f)*M_PI/N_f;
time_H[n] += omega_H[k]*(cos(omega_k*t_n));
}
time_H[n]/=(2.0*N_f);
}
}
//update the colored random force every alpha MD steps
if (counter_mu == 0) {
//propagate h_timestep ahead
for (int j = 0; j < nlocal; j++) {
//update random array
for (int m = 0; m < 2*N_f-1; m++) {
random_array_0[j][m] = random_array_0[j][m+1];
random_array_1[j][m] = random_array_1[j][m+1];
random_array_2[j][m] = random_array_2[j][m+1];
}
random_array_0[j][2*N_f-1] = random->uniform()-0.5;
random_array_1[j][2*N_f-1] = random->uniform()-0.5;
random_array_2[j][2*N_f-1] = random->uniform()-0.5;
//reset random force
fran[j][0] = 0.0;
fran[j][1] = 0.0;
fran[j][2] = 0.0;
if (mask[j] & groupbit) {
double gamma3 = gfactor[type[j]];
for (int m = 0; m < 2*N_f; m++) {
fran[j][0] += time_H[m] * random_array_0[j][2*N_f-m-1];
fran[j][1] += time_H[m] * random_array_1[j][2*N_f-m-1];
fran[j][2] += time_H[m] * random_array_2[j][2*N_f-m-1];
}
fran[j][0] = fran[j][0]*gamma3;
fran[j][1] = fran[j][1]*gamma3;
fran[j][2] = fran[j][2]*gamma3;
}
}
}
// estimate old energy average in this step
old_eavg = old_eavg + compute_egrand()/beta;
counter_l = (counter_l + 1) % beta;
counter_mu = (counter_mu + 1) % alpha;
// propagate the time derivative of
// the volume 1/2 step at fixed vol, r, rdot.
p_qbmsst = nktv2p * mvv2e * velocity * velocity * total_mass *
( v0 - vol)/( v0 * v0);
double A = total_mass * ( p_current[sd] - p0 - p_qbmsst ) /
(qmass * nktv2p * mvv2e);
double B = total_mass * mu / ( qmass * vol );
// prevent blow-up of the volume.
if ( vol > v0 && A > 0.0 ) {
A = -A;
}
// use taylor expansion to avoid singularity at B == 0.
if ( B * dthalf > 1.0e-06 ) {
omega[sd] = ( omega[sd] + A * ( exp(B * dthalf) - 1.0 ) / B )
* exp(-B * dthalf);
} else {
omega[sd] = omega[sd] + (A - B * omega[sd]) * dthalf +
0.5 * (B * B * omega[sd] - A * B ) * dthalf * dthalf;
}
// propagate velocity sum 1/2 step by
// temporarily propagating the velocities.
velocity_sum = compute_vsum();
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
double C = (f[i][k] + fran[i][k])* force->ftm2v / mass[type[i]];// this term now has a random force part
double D = mu * omega[sd] * omega[sd] /
(velocity_sum * mass[type[i]] * vol ) - fric_coef;
old_velocity[i][k] = v[i][k];
if ( k == direction ) {
D = D - 2.0 * omega[sd] / vol;
}
if ( fabs(dthalf * D) > 1.0e-06 ) {
double expd = exp(D * dthalf);
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
} else {
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
}
}
}
}
velocity_sum = compute_vsum();
// reset the velocities.
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
v[i][k] = old_velocity[i][k];
}
}
}
// propagate velocities 1/2 step using the new velocity sum.
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( k = 0; k < 3; k++ ) {
double C = (f[i][k] + fran[i][k])* force->ftm2v / mass[type[i]];// this term now has a random force part
double D = mu * omega[sd] * omega[sd] /
(velocity_sum * mass[type[i]] * vol ) - fric_coef;
if ( k == direction ) {
D = D - 2.0 * omega[sd] / vol;
}
if ( fabs(dthalf * D) > 1.0e-06 ) {
double expd = exp(D * dthalf);
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
} else {
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
}
}
}
}
// propagate the volume 1/2 step.
double vol1 = vol + omega[sd] * dthalf;
// rescale positions and change box size.
dilation[sd] = vol1/vol;
remap(0);
// propagate particle positions 1 time step.
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
}
}
// propagate the volume 1/2 step.
double vol2 = vol1 + omega[sd] * dthalf;
// rescale positions and change box size.
dilation[sd] = vol2/vol1;
remap(0);
if (kspace_flag) force->kspace->setup();
}
/* ----------------------------------------------------------------------
2nd half of Verlet update
------------------------------------------------------------------------- */
void FixQBMSST::final_integrate()
{
int i;
// v update only for atoms in QBMSST group
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double vol = compute_vol();
double p_qbmsst;
int sd = direction;
// propagate particle velocities 1/2 step.
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
for ( int k = 0; k < 3; k++ ) {
double C = (f[i][k] + fran[i][k]) * force->ftm2v / mass[type[i]];// this term now has a random force part
double D = mu * omega[sd] * omega[sd] /
(velocity_sum * mass[type[i]] * vol ) - fric_coef;
if ( k == direction ) {
D = D - 2.0 * omega[sd] / vol;
}
if ( fabs(dthalf * D) > 1.0e-06 ) {
double expd = exp(D * dthalf);
v[i][k] = expd * ( C + D * v[i][k] - C / expd ) / D;
} else {
v[i][k] = v[i][k] + ( C + D * v[i][k] ) * dthalf +
0.5 * (D * D * v[i][k] + C * D ) * dthalf * dthalf;
}
}
}
}
// compute new pressure and volume.
temperature->compute_vector();
pressure->compute_vector();
couple();
velocity_sum = compute_vsum();
vol = compute_vol();
// propagate the time derivative of the volume 1/2 step at fixed V, r, rdot.
p_qbmsst = nktv2p * mvv2e * velocity * velocity * total_mass *
( v0 - vol )/( v0 * v0 );
double A = total_mass * ( p_current[sd] - p0 - p_qbmsst ) /
( qmass * nktv2p * mvv2e );
double B = total_mass * mu / ( qmass * vol );
// prevent blow-up of the volume.
if ( vol > v0 && A > 0.0 ) {
A = -A;
}
// use taylor expansion to avoid singularity at B == 0.
if ( B * dthalf > 1.0e-06 ) {
omega[sd] = ( omega[sd] + A *
( exp(B * dthalf) - 1.0 ) / B ) * exp(-B * dthalf);
} else {
omega[sd] = omega[sd] + (A - B * omega[sd]) * dthalf +
0.5 * (B * B * omega[sd] - A * B ) * dthalf * dthalf;
}
// calculate Lagrangian position of computational cell
lagrangian_position -= velocity*vol/v0*update->dt;
// trigger virial computation on next timestep
pressure->addstep(update->ntimestep+1);
pe->addstep(update->ntimestep+1);
}
/* ----------------------------------------------------------------------
couple
------------------------------------------------------------------------- */
void FixQBMSST::couple()
{
double *tensor = pressure->vector;
p_current[0] = tensor[0];
p_current[1] = tensor[1];
p_current[2] = tensor[2];
}
/* ----------------------------------------------------------------------
change box size
remap owned or owned+ghost atoms depending on flag
if rigid bodies exist, scale rigid body centers-of-mass
------------------------------------------------------------------------- */
void FixQBMSST::remap(int flag)
{
int i,n;
double oldlo,oldhi,ctr;
double **v = atom->v;
if (flag) n = atom->nlocal + atom->nghost;
else n = atom->nlocal;
// convert pertinent atoms and rigid bodies to lamda coords
domain->x2lamda(n);
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(0);
// reset global and local box to new size/shape
for (i = 0; i < 3; i++) {
if ( direction == i ) {
oldlo = domain->boxlo[i];
oldhi = domain->boxhi[i];
ctr = 0.5 * (oldlo + oldhi);
domain->boxlo[i] = (oldlo-ctr)*dilation[i] + ctr;
domain->boxhi[i] = (oldhi-ctr)*dilation[i] + ctr;
}
}
domain->set_global_box();
domain->set_local_box();
// convert pertinent atoms and rigid bodies back to box coords
domain->lamda2x(n);
if (nrigid)
for (i = 0; i < nrigid; i++)
modify->fix[rfix[i]]->deform(1);
for (i = 0; i < n; i++) {
v[i][direction] = v[i][direction] *
dilation[direction];
}
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixQBMSST::write_restart(FILE *fp)
{
int n = 0;
double list[5];
list[n++] = omega[direction];
list[n++] = e0;
list[n++] = v0;
list[n++] = p0;
list[n++] = t_current;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(&list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixQBMSST::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
omega[direction] = list[n++];
e0 = list[n++];
v0 = list[n++];
p0 = list[n++];
t_current = list[n++];
e0_set = 1;
v0_set = 1;
p0_set = 1;
qtb_set = 1;
}
/* ----------------------------------------------------------------------
modify parameters
------------------------------------------------------------------------- */
int FixQBMSST::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 != 0 && comm->me == 0)
error->warning(FLERR,"Temperature for QBMSST is not for group all");
return 2;
} else if (strcmp(arg[0],"press") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (pflag) {
modify->delete_compute(id_press);
pflag = 0;
}
delete [] id_press;
int n = strlen(arg[1]) + 1;
id_press = new char[n];
strcpy(id_press,arg[1]);
int icompute = modify->find_compute(id_press);
if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
pressure = modify->compute[icompute];
if (pressure->pressflag == 0)
error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
compute scalar
------------------------------------------------------------------------- */
double FixQBMSST::compute_scalar()
{
// compute new pressure and volume.
temperature->compute_vector();
pressure->compute_vector();
couple();
double volume = compute_vol();
double energy = 0.0;
int i;
i = direction;
energy = qmass * omega[i] * omega[i] / (2.0 * total_mass) * mvv2e;
energy -= 0.5 * total_mass * velocity * velocity *
(1.0 - volume/ v0) *
(1.0 - volume/ v0) * mvv2e;
energy -= p0 * ( v0 - volume ) / nktv2p;
return energy;
}
/* ----------------------------------------------------------------------
return a single element from the following vector,
[dhug,dray,lgr_vel,lgr_pos,T_qm]
------------------------------------------------------------------------- */
double FixQBMSST::compute_vector(int n)
{
if (n == 0) {
return compute_hugoniot();
} else if (n == 1) {
return compute_rayleigh();
} else if (n == 2) {
return compute_lagrangian_speed();
} else if (n == 3) {
return compute_lagrangian_position();
} else if (n == 4) {
return t_current;
}
return 0.0;
}
/* ----------------------------------------------------------------------
Computes the deviation of the current point
from the Hugoniot in Kelvin for the QBMSST.
------------------------------------------------------------------------- */
double FixQBMSST::compute_hugoniot()
{
double v, e, p;
double dhugo;
e = compute_etotal();
temperature->compute_vector();
pressure->compute_vector();
p = pressure->vector[direction];
v = compute_vol();
dhugo = (0.5 * (p + p0 ) * ( v0 - v)) /
force->nktv2p + e0 - e;
dhugo /= temperature->dof * force->boltz;
return dhugo;
}
/* ----------------------------------------------------------------------
Computes the deviation of the current point from the Rayleigh
in pressure units for the QBMSST.
------------------------------------------------------------------------- */
double FixQBMSST::compute_rayleigh()
{
double v, p;
double drayleigh;
temperature->compute_vector();
pressure->compute_vector();
p = pressure->vector[direction];
v = compute_vol();
drayleigh = p - p0 -
total_mass * velocity * velocity * force->mvv2e *
(1.0 - v / v0 ) * force->nktv2p / v0;
return drayleigh;
}
/* ----------------------------------------------------------------------
Computes the speed of the QBMSST computational cell in the
unshocked material rest-frame
------------------------------------------------------------------------- */
double FixQBMSST::compute_lagrangian_speed()
{
double v = compute_vol();
return velocity*(1.0-v/v0);
}
/* ----------------------------------------------------------------------
Computes the distance behind the
shock front of the QBMSST computational cell.
------------------------------------------------------------------------- */
double FixQBMSST::compute_lagrangian_position()
{
return lagrangian_position;
}
/* ----------------------------------------------------------------------
Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
external potential terms in the QBMSST Lagrangian.
------------------------------------------------------------------------- */
double FixQBMSST::compute_etotal()
{
double epot,ekin,etot;
epot = pe->compute_scalar();
if (thermo_energy) epot -= compute_scalar();
ekin = temperature->compute_scalar();
ekin *= 0.5 * temperature->dof * force->boltz;
etot = epot+ekin;
return etot;
}
/* ----------------------------------------------------------------------
Computes the atomic kinetic + atomic potential energy + QBMSST external potential.
------------------------------------------------------------------------- */
double FixQBMSST::compute_egrand()
{
double epot,ekin,etot;
epot = pe->compute_scalar();
if (!thermo_energy) epot += compute_scalar();
ekin = temperature->compute_scalar();
ekin *= 0.5 * temperature->dof * force->boltz;
etot = epot+ekin;
return etot;
}
/* ----------------------------------------------------------------------
Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
external potential terms in the QBMSST Lagrangian.
------------------------------------------------------------------------- */
double FixQBMSST::compute_vol()
{
if (domain->dimension == 3)
return domain->xprd * domain->yprd * domain->zprd;
else
return domain->xprd * domain->yprd;
}
/* ----------------------------------------------------------------------
Checks to see if the allocated size of old_velocity is >= n
The number of local atoms can change during a parallel run.
------------------------------------------------------------------------- */
void FixQBMSST::check_alloc(int n)
{
if ( atoms_allocated < n ) {
memory->destroy(old_velocity);
memory->create(old_velocity,n,3,"qbmsst:old_velocity");
atoms_allocated = n;
}
}
/* ----------------------------------------------------------------------
Computes the atomic kinetic + atomic potential energy. This excludes the QBMSST
external potential terms in the QBMSST Lagrangian.
------------------------------------------------------------------------- */
double FixQBMSST::compute_vsum()
{
double vsum;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double t = 0.0;
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]) ;
}
}
MPI_Allreduce(&t,&vsum,1,MPI_DOUBLE,MPI_SUM,world);
return vsum;
}
/* ----------------------------------------------------------------------
memory usage of fix qbmsst
------------------------------------------------------------------------- */
double FixQBMSST::memory_usage()
{
double bytes = 0.0;
// random_arrays memory usage
bytes += (atom->nmax* 6*N_f * sizeof(double));
// fran memory usage
bytes += (atom->nmax* 3 * sizeof(double));
bytes += (4*N_f * sizeof(double));
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array for fran and random_array
------------------------------------------------------------------------- */
void FixQBMSST::grow_arrays(int nmax)
{
memory->grow(random_array_0,nmax,2*N_f,"qbmsst:random_array_0");
memory->grow(random_array_1,nmax,2*N_f,"qbmsst:random_array_1");
memory->grow(random_array_2,nmax,2*N_f,"qbmsst:random_array_2");
memory->grow(fran,nmax,3,"qbmsst:fran");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixQBMSST::copy_arrays(int i, int j, int delflag)
{
for (int m = 0; m < 2*N_f; m++) {
random_array_0[j][m] = random_array_0[i][m];
random_array_1[j][m] = random_array_1[i][m];
random_array_2[j][m] = random_array_2[i][m];
}
for (int m = 0; m < 3; m++)
fran[j][m] = fran[i][m];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixQBMSST::pack_exchange(int i, double *buf)
{
for (int m = 0; m < 2*N_f; m++) buf[m] = random_array_0[i][m];
for (int m = 0; m < 2*N_f; m++) buf[m+2*N_f] = random_array_1[i][m];
for (int m = 0; m < 2*N_f; m++) buf[m+4*N_f] = random_array_2[i][m];
for (int m = 0; m < 3; m++) buf[m+6*N_f] = fran[i][m];
return 6*N_f+3;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixQBMSST::unpack_exchange(int nlocal, double *buf)
{
for (int m = 0; m < 2*N_f; m++) random_array_0[nlocal][m] = buf[m];
for (int m = 0; m < 2*N_f; m++) random_array_1[nlocal][m] = buf[m+2*N_f];
for (int m = 0; m < 2*N_f; m++) random_array_2[nlocal][m] = buf[m+4*N_f];
for (int m = 0; m < 3; m++) fran[nlocal][m] = buf[m+6*N_f];
return 6*N_f+3;
}

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