void thermo_init_npt_isotropic()
{
if (nptiso.piston != 0.0) {
#if defined (FLATNOISE)
nptiso_pref1 = -nptiso_gamma0*0.5 * time_step;
#ifdef MULTI_TIMESTEP
if (smaller_time_step > 0.)
nptiso_pref2 = sqrt(12.0*temperature*nptiso_gamma0*time_step) * smaller_time_step;
else
#endif
nptiso_pref2 = sqrt(12.0*temperature*nptiso_gamma0*time_step) * time_step;
nptiso_pref3 = -nptiso_gammav*(1.0/nptiso.piston)*0.5*time_step;
nptiso_pref4 = sqrt(12.0*temperature*nptiso_gammav*time_step);
#elif defined (GAUSSRANDOMCUT) || defined (GAUSSRANDOM)
nptiso_pref1 = -nptiso_gamma0*0.5 * time_step;
nptiso_pref2 = sqrt(1.0*temperature*nptiso_gamma0*time_step) * time_step;
nptiso_pref3 = -nptiso_gammav*(1.0/nptiso.piston)*0.5*time_step;
nptiso_pref4 = sqrt(1.0*temperature*nptiso_gammav*time_step);
#else
#error No Noise defined
#endif
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_npt_isotropic: nptiso_pref1=%f, nptiso_pref2=%f, nptiso_pref3=%f, nptiso_pref4=%f \n",this_node,nptiso_pref1,nptiso_pref2,nptiso_pref3,nptiso_pref4));
}
else {
thermo_switch = ( thermo_switch ^ THERMO_NPT_ISO );
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_npt_isotropic: switched off nptiso (piston=%f; thermo_switch=%d) \n",this_node,nptiso.piston,thermo_switch));
}
}
void thermo_init_dpd()
{
extern double dpd_gamma,dpd_r_cut,dpd_pref1,dpd_pref2;
/*extern int dpd_wf;*/
#ifdef TRANS_DPD
extern double dpd_tgamma,dpd_tr_cut,dpd_pref3,dpd_pref4;
/*extern int dpd_twf;*/
#endif
/* prefactor friction force */
/* NOTE: velocities are scaled with time_step, so divide by time_step here*/
dpd_pref1 = dpd_gamma/time_step;
/* prefactor random force */
/*NOTE random force is propto sqrt(time_step)*/
dpd_pref2 = sqrt(24.0*temperature*dpd_gamma/time_step);
dpd_r_cut_inv = 1.0/dpd_r_cut;
#ifdef TRANS_DPD
/* NOTE: velocities are scaled with time_step, so divide by time_step here*/
dpd_pref3 = dpd_tgamma/time_step;
/*NOTE random force is propto sqrt(time_step)*/
dpd_pref4 = sqrt(24.0*temperature*dpd_tgamma/time_step);
dpd_tr_cut_inv = 1.0/dpd_tr_cut;
#endif
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_dpd: dpd_pref1=%f, dpd_pref2=%f",
this_node,dpd_pref1,dpd_pref2));
#ifdef TRANS_DPD
THERMO_TRACE(fprintf(stderr,",dpd_pref3=%f, dpd_pref4=%f\n",dpd_pref3,dpd_pref4));
#endif
THERMO_TRACE(fprintf(stderr,"\n"));
}
void thermo_init_langevin()
{
int j;
langevin_pref1 = -langevin_gamma/time_step;
#if defined (FLATNOISE)
langevin_pref2 = sqrt(24.0*temperature*langevin_gamma/time_step);
#elif defined (GAUSSRANDOMCUT) || defined (GAUSSRANDOM)
langevin_pref2 = sqrt(2.0*temperature*langevin_gamma/time_step);
#else
#error No Noise defined
#endif
#ifdef MULTI_TIMESTEP
if (smaller_time_step > 0.) {
langevin_pref1_small = -langevin_gamma/smaller_time_step;
#ifndef LANGEVIN_PER_PARTICLE
langevin_pref2_small = sqrt(24.0*temperature*langevin_gamma/smaller_time_step);
#endif
} else {
langevin_pref1_small = -langevin_gamma/time_step;
#ifndef LANGEVIN_PER_PARTICLE
langevin_pref2_small = sqrt(24.0*temperature*langevin_gamma/time_step);
#endif
}
#endif
#ifdef ROTATION
#ifndef ROTATIONAL_INERTIA
if ( langevin_gamma_rotation < 0.0 )
{
langevin_gamma_rotation = langevin_gamma;
}
#else
if (( langevin_gamma_rotation[0] < 0.0 ) || (langevin_gamma_rotation[1] < 0.0) || (langevin_gamma_rotation[2] < 0.0))
for ( j = 0 ; j < 3 ; j++)
{
langevin_gamma_rotation[j] = langevin_gamma;
}
#endif
#ifndef ROTATIONAL_INERTIA
#if defined (FLATNOISE)
langevin_pref2_rotation = sqrt(24.0*temperature*langevin_gamma_rotation/time_step);
#elif defined (GAUSSRANDOMCUT) || defined (GAUSSRANDOM)
langevin_pref2_rotation = sqrt(2.0*temperature*langevin_gamma_rotation/time_step);
#else
#error No Noise defined
#endif
#else
#if defined (FLATNOISE)
for ( j = 0 ; j < 3 ; j++) langevin_pref2_rotation[j] = sqrt(24.0*temperature*langevin_gamma_rotation[j]/time_step);
#elif defined (GAUSSRANDOMCUT) || defined (GAUSSRANDOM)
for ( j = 0 ; j < 3 ; j++) langevin_pref2_rotation[j] = sqrt(2.0*temperature*langevin_gamma_rotation[j]/time_step);
#else
#error No Noise defined
#endif
#endif // ROTATIONAL_INERTIA
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_langevin: langevin_gamma_rotation=%f, langevin_pref2_rotation=%f",this_node, langevin_gamma_rotation,langevin_pref2_rotation));
#endif
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_langevin: langevin_pref1=%f, langevin_pref2=%f",this_node,langevin_pref1,langevin_pref2));
}
int tclcommand_ghmc(ClientData data, Tcl_Interp *interp, int argc, char **argv)
{
#ifdef GHMC
int status = TCL_OK;
THERMO_TRACE(fprintf(stderr,"%d: ghmc:\n",this_node));
Tcl_ResetResult(interp);
/* print ghmc status */
if(argc == 1) {
status = tclcommand_ghmc_print_status(interp) ;
}
else if (ARG1_IS_S("statistics")) {
status = tclcommand_ghmc_print_statistics(interp);
}
else {
Tcl_AppendResult(interp, "Unknown keyword: \n", (char *)NULL);
status = tclcommand_ghmc_print_usage(interp);
}
return status;
#else
INTEG_TRACE(fprintf(stderr,"%d: call to ghmc but not compiled in!\n",this_node));
return tclcommand_ghmc_print_usage(interp);
#endif
}
/** set the particle torques to the friction term, i.e. \f$\tau_i=-\gamma w_i + \xi_i\f$.
The same friction coefficient \f$\gamma\f$ is used as that for translation.
*/
inline void friction_thermo_langevin_rotation(Particle *p)
{
extern double langevin_pref2_rotation;
int j;
double switch_rotate = 1.0;
if ( langevin_rotate == false )
{
switch_rotate = 0.0;
}
// Rotational degrees of virtual sites are thermostatted,
// so no switching here
// Here the thermostats happens
for ( j = 0 ; j < 3 ; j++)
{
#ifdef ROTATIONAL_INERTIA
p->f.torque[j] = -langevin_gamma_rotation*p->m.omega[j] + switch_rotate*langevin_pref2_rotation*noise;
#else
p->f.torque[j] = -langevin_gamma_rotation*p->m.omega[j] + switch_rotate*langevin_pref2_rotation*noise;
#endif
}
ONEPART_TRACE(if(p->p.identity==check_id) fprintf(stderr,"%d: OPT: LANG f = (%.3e,%.3e,%.3e)\n",this_node,p->f.f[0],p->f.f[1],p->f.f[2]));
THERMO_TRACE(fprintf(stderr,"%d: Thermo: P %d: force=(%.3e,%.3e,%.3e)\n",this_node,p->p.identity,p->f.f[0],p->f.f[1],p->f.f[2]));
}
int tclcommand_thermostat(ClientData data, Tcl_Interp *interp, int argc, char **argv)
{
int err = TCL_OK;
THERMO_TRACE(fprintf(stderr,"%d: thermostat:\n",this_node));
/* print thermostat status */
if(argc == 1) return tclcommand_thermostat_print_all(interp);
if ( ARG1_IS_S("set") ) {
argc--;
argv++;
if (argc == 1) {
Tcl_AppendResult(interp, "wrong # args: \n", (char *)NULL);
return tclcommand_thermostat_print_usage(interp, argc, argv);
}
}
if ( ARG1_IS_S("off") )
err = tclcommand_thermostat_parse_off(interp, argc, argv);
else if ( ARG1_IS_S("langevin"))
err = tclcommand_thermostat_parse_langevin(interp, argc, argv);
#ifdef DPD
else if ( ARG1_IS_S("dpd") )
err = tclcommand_thermostat_parse_dpd(interp, argc, argv);
#endif
#ifdef INTER_DPD
else if ( ARG1_IS_S("inter_dpd") )
err = tclcommand_thermostat_parse_inter_dpd(interp, argc, argv);
#endif
#ifdef NPT
else if ( ARG1_IS_S("npt_isotropic") )
err = tclcommand_thermostat_parse_npt_isotropic(interp, argc, argv);
#endif
#if defined(LB) || defined(LB_GPU)
else if ( ARG1_IS_S("lb"))
err = tclcommand_thermostat_parse_lb(interp, argc-1, argv+1);
#endif
#ifdef GHMC
else if ( ARG1_IS_S("ghmc") )
err = tclcommand_thermostat_parse_ghmc(interp, argc, argv);
#endif
else if ( ARG1_IS_S("cpu"))
err = tclcommand_thermostat_parse_cpu(interp, argc, argv);
#if defined(SD) || defined(BD)
#ifdef SD
else if ( ARG1_IS_S("sd") )
err = tclcommand_thermostat_parse_sd(interp, argc, argv);
#endif // SD
else if ( ARG1_IS_S("bd") )
err = tclcommand_thermostat_parse_bd(interp, argc, argv);
#endif //SD || BD
else {
Tcl_AppendResult(interp, "Unknown thermostat ", argv[1], "\n", (char *)NULL);
return tclcommand_thermostat_print_usage(interp, argc, argv);
}
return gather_runtime_errors(interp, err);
}
void thermo_init_ghmc()
{
ghmc_att=0;
ghmc_acc=0;
cosp = ghmc_phi;
sinp = sin(acos(ghmc_phi));
ghmcdata.hmlt_old=0;
ghmcdata.hmlt_new=0;
beta=1.0/temperature;
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_ghmc: ghmc_csp=%f, ghmc_snp=%f \n",this_node,cosp,sinp));
}
void thermo_init_langevin()
{
langevin_pref1 = -langevin_gamma/time_step;
#if defined (FLATNOISE)
langevin_pref2 = sqrt(24.0*temperature*langevin_gamma/time_step);
#elif defined (GAUSSRANDOMCUT) || defined (GAUSSRANDOM)
langevin_pref2 = sqrt(2.0*temperature*langevin_gamma/time_step);
#else
#error No Noise defined
#endif
#ifdef MULTI_TIMESTEP
if (smaller_time_step > 0.) {
langevin_pref1_small = -langevin_gamma/smaller_time_step;
#ifndef LANGEVIN_PER_PARTICLE
langevin_pref2_small = sqrt(24.0*temperature*langevin_gamma/smaller_time_step);
#endif
} else {
langevin_pref1_small = -langevin_gamma/time_step;
#ifndef LANGEVIN_PER_PARTICLE
langevin_pref2_small = sqrt(24.0*temperature*langevin_gamma/time_step);
#endif
}
#endif
#ifdef ROTATION
langevin_gamma_rotation = langevin_gamma/3;
#if defined (FLATNOISE)
langevin_pref2_rotation = sqrt(24.0*temperature*langevin_gamma_rotation/time_step);
#elif defined (GAUSSRANDOMCUT) || defined (GAUSSRANDOM)
langevin_pref2_rotation = sqrt(2.0*temperature*langevin_gamma_rotation/time_step);
#else
#error No Noise defined
#endif
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_langevin: langevin_gamma_rotation=%f, langevin_pref2_rotation=%f",this_node, langevin_gamma_rotation,langevin_pref2_rotation));
#endif
THERMO_TRACE(fprintf(stderr,"%d: thermo_init_langevin: langevin_pref1=%f, langevin_pref2=%f",this_node,langevin_pref1,langevin_pref2));
}
/** overwrite the forces of a particle with
the friction term, i.e. \f$ F_i= -\gamma v_i + \xi_i\f$.
*/
inline void friction_thermo_langevin(Particle *p)
{
extern double langevin_pref1, langevin_pref2;
double langevin_pref1_temp, langevin_pref2_temp;
#ifdef MULTI_TIMESTEP
extern double langevin_pref1_small;
#ifndef LANGEVIN_PER_PARTICLE
extern double langevin_pref2_small;
#endif /* LANGEVIN_PER_PARTICLE */
#endif /* MULTI_TIMESTEP */
int j;
double switch_trans = 1.0;
if ( langevin_trans == false )
{
switch_trans = 0.0;
}
// Virtual sites related decision making
#ifdef VIRTUAL_SITES
#ifndef VIRTUAL_SITES_THERMOSTAT
// In this case, virtual sites are NOT thermostated
if (ifParticleIsVirtual(p))
{
for (j=0; j<3; j++)
p->f.f[j]=0;
return;
}
#endif /* VIRTUAL_SITES_THERMOSTAT */
#ifdef THERMOSTAT_IGNORE_NON_VIRTUAL
// In this case NON-virtual particles are NOT thermostated
if (!ifParticleIsVirtual(p))
{
for (j=0; j<3; j++)
p->f.f[j]=0;
return;
}
#endif /* THERMOSTAT_IGNORE_NON_VIRTUAL */
#endif /* VIRTUAL_SITES */
// Get velocity effective in the thermostatting
double velocity[3];
for (int i = 0; i < 3; i++) {
// Particle velocity
velocity[i] = p->m.v[i];
#ifdef ENGINE
// In case of the engine feature, the velocity is relaxed
// towards a swimming velocity oriented parallel to the
// particles director
velocity[i] -= (p->swim.v_swim*time_step)*p->r.quatu[i];
#endif
// Local effective velocity for leeds-edwards boundary conditions
velocity[i]=le_frameV(i,velocity,p->r.p);
} // for
// Determine prefactors for the friction and the noise term
// first, set defaults
langevin_pref1_temp = langevin_pref1;
langevin_pref2_temp = langevin_pref2;
// Override defaults if per-particle values for T and gamma are given
#ifdef LANGEVIN_PER_PARTICLE
// If a particle-specific gamma is given
if(p->p.gamma >= 0.)
{
langevin_pref1_temp = -p->p.gamma/time_step;
// Is a particle-specific temperature also specified?
if(p->p.T >= 0.)
langevin_pref2_temp = sqrt(24.0*p->p.T*p->p.gamma/time_step);
else
// Default temperature but particle-specific gamma
langevin_pref2_temp = sqrt(24.0*temperature*p->p.gamma/time_step);
} // particle specific gamma
else
{
langevin_pref1_temp = -langevin_gamma/time_step;
// No particle-specific gamma, but is there particle-specific temperature
if(p->p.T >= 0.)
langevin_pref2_temp = sqrt(24.0*p->p.T*langevin_gamma/time_step);
else
// Defaut values for both
langevin_pref2_temp = langevin_pref2;
}
#endif /* LANGEVIN_PER_PARTICLE */
// Multi-timestep handling
// This has to be last, as it may set the prefactors to 0.
#ifdef MULTI_TIMESTEP
if (smaller_time_step > 0.) {
langevin_pref1_temp *= time_step/smaller_time_step;
if (p->p.smaller_timestep==1 && current_time_step_is_small==1)
langevin_pref2_temp *= sqrt(time_step/smaller_time_step);
else if (p->p.smaller_timestep != current_time_step_is_small) {
langevin_pref1_temp = 0.;
langevin_pref2_temp = 0.;
}
}
#endif /* MULTI_TIMESTEP */
// Do the actual thermostatting
for ( j = 0 ; j < 3 ; j++)
{
#ifdef EXTERNAL_FORCES
// If individual coordinates are fixed, set force to 0.
if ((p->p.ext_flag & COORD_FIXED(j)))
p->f.f[j] = 0;
else
#endif
{
// Apply the force
p->f.f[j] = langevin_pref1_temp*velocity[j] + switch_trans*langevin_pref2_temp*noise;
}
} // END LOOP OVER ALL COMPONENTS
// printf("%d: %e %e %e %e %e %e\n",p->p.identity, p->f.f[0],p->f.f[1],p->f.f[2], p->m.v[0],p->m.v[1],p->m.v[2]);
ONEPART_TRACE(if(p->p.identity==check_id) fprintf(stderr,"%d: OPT: LANG f = (%.3e,%.3e,%.3e)\n",this_node,p->f.f[0],p->f.f[1],p->f.f[2]));
THERMO_TRACE(fprintf(stderr,"%d: Thermo: P %d: force=(%.3e,%.3e,%.3e)\n",this_node,p->p.identity,p->f.f[0],p->f.f[1],p->f.f[2]));
}
