void energy_calc(double *result)
{
if (!check_obs_calc_initialized())
return;
init_energies(&energy);
on_observable_calc();
switch (cell_structure.type) {
case CELL_STRUCTURE_LAYERED:
layered_calculate_energies();
break;
case CELL_STRUCTURE_DOMDEC:
if(dd.use_vList) {
if (rebuild_verletlist)
build_verlet_lists();
calculate_verlet_energies();
}
else
calculate_link_cell_energies();
break;
case CELL_STRUCTURE_NSQUARE:
nsq_calculate_energies();
}
/* rescale kinetic energy */
energy.data.e[0] /= (2.0*time_step*time_step);
calc_long_range_energies();
/* gather data */
MPI_Reduce(energy.data.e, result, energy.data.n, MPI_DOUBLE, MPI_SUM, 0, comm_cart);
}
void on_integration_start()
{
char *errtext;
EVENT_TRACE(fprintf(stderr, "%d: on_integration_start\n", this_node));
INTEG_TRACE(fprintf(stderr,"%d: on_integration_start: reinit_thermo = %d, resort_particles=%d\n",
this_node,reinit_thermo,resort_particles));
/********************************************/
/* sanity checks */
/********************************************/
if ( time_step < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext, "{010 time_step not set} ");
}
if ( skin < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{011 skin not set} ");
}
if ( temperature < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{012 thermostat not initialized} ");
}
#ifdef NPT
if (integ_switch == INTEG_METHOD_NPT_ISO) {
if (nptiso.piston <= 0.0) {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt on, but piston mass not set} ");
}
#ifdef ELECTROSTATICS
switch(coulomb.method) {
case COULOMB_NONE:
break;
#ifdef P3M
case COULOMB_P3M:
break;
#endif /*P3M*/
default: {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt only works with P3M} ");
}
}
#endif /*ELECTROSTATICS*/
#ifdef DIPOLES
switch (coulomb.Dmethod) {
case DIPOLAR_NONE:
break;
#ifdef DP3M
case DIPOLAR_P3M:
break;
#endif
default: {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"NpT does not work with your dipolar method, please use P3M.");
}
}
#endif /* ifdef DIPOLES */
}
#endif /*NPT*/
if (!check_obs_calc_initialized()) return;
#ifdef LB
if(lattice_switch & LATTICE_LB) {
if (lbpar.agrid <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{098 Lattice Boltzmann agrid not set} ");
}
if (lbpar.tau <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{099 Lattice Boltzmann time step not set} ");
}
if (lbpar.rho <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{100 Lattice Boltzmann fluid density not set} ");
}
if (lbpar.viscosity <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{101 Lattice Boltzmann fluid viscosity not set} ");
}
if (dd.use_vList && skin>=lbpar.agrid/2.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext, "{104 LB requires either no Verlet lists or that the skin of the verlet list to be less than half of lattice-Boltzmann grid spacing.} ");
}
}
#endif
#ifdef LB_GPU
if(this_node == 0) {
if(lattice_switch & LATTICE_LB_GPU) {
if (lbpar_gpu.agrid < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{098 Lattice Boltzmann agrid not set} ");
}
if (lbpar_gpu.tau < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{099 Lattice Boltzmann time step not set} ");
}
if (lbpar_gpu.rho < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{100 Lattice Boltzmann fluid density not set} ");
}
if (lbpar_gpu.viscosity < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{101 Lattice Boltzmann fluid viscosity not set} ");
}
if (lb_reinit_particles_gpu) {
lb_realloc_particles_gpu();
lb_reinit_particles_gpu = 0;
}
}
}
#endif
#ifdef METADYNAMICS
meta_init();
#endif
#ifdef REACTIONS
if(reaction.rate != 0.0) {
if(max_cut < reaction.range) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{105 Reaction range of %f exceeds maximum cutoff of %f} ", reaction.range, max_cut);
}
}
#endif
/********************************************/
/* end sanity checks */
/********************************************/
/* Prepare the thermostat */
if (reinit_thermo) {
thermo_init();
reinit_thermo = 0;
recalc_forces = 1;
}
/* Ensemble preparation: NVT or NPT */
integrate_ensemble_init();
#ifdef SCAFACOS
/* initialize Scafacos, set up the system and solver specific parameters, all on
each node. functions include MPI_Bcast */
mpi_bcast_coulomb_method();
switch(coulomb.method) {
case COULOMB_SCAFACOS_DIRECT:
case COULOMB_SCAFACOS_EWALD:
case COULOMB_SCAFACOS_FMM:
case COULOMB_SCAFACOS_MEMD:
case COULOMB_SCAFACOS_MMM1D:
case COULOMB_SCAFACOS_MMM2D:
case COULOMB_SCAFACOS_P2NFFT:
case COULOMB_SCAFACOS_P3M:
case COULOMB_SCAFACOS_PEPC:
case COULOMB_SCAFACOS_PP3MG:
case COULOMB_SCAFACOS_VMG: {
mpi_scafacos_bcast_common_params();
mpi_scafacos_bcast_solver_specific();
mpi_scafacos_init();
mpi_scafacos_common_set();
mpi_scafacos_solver_specific_set();
break;
}
default:
break;
}
/* tune in order to generate at least defaults for cutoff, transfer the cutoff back
to Espresso and generate new cell system on each node*/
switch(coulomb.method) {
case COULOMB_SCAFACOS_P2NFFT:
if( scafacos.short_range_flag == 0 ) {
scafacos_tune();
recalc_maximal_cutoff();
cells_on_geometry_change(0);
}
break;
case COULOMB_SCAFACOS_P3M:
if( scafacos.short_range_flag == 0 ) {
scafacos_tune();
recalc_maximal_cutoff();
cells_on_geometry_change(0);
}
default:
break;
}
#endif
/* Update particle and observable information for routines in statistics.c */
invalidate_obs();
freePartCfg();
on_observable_calc();
}
void pressure_calc(double *result, double *result_t, double *result_nb, double *result_t_nb, int v_comp)
{
int n, i;
double volume = box_l[0]*box_l[1]*box_l[2];
if (!check_obs_calc_initialized())
return;
init_virials(&virials);
init_p_tensor(&p_tensor);
init_virials_non_bonded(&virials_non_bonded);
init_p_tensor_non_bonded(&p_tensor_non_bonded);
on_observable_calc();
switch (cell_structure.type) {
case CELL_STRUCTURE_LAYERED:
layered_calculate_virials(v_comp);
break;
case CELL_STRUCTURE_DOMDEC:
if(dd.use_vList) {
if (rebuild_verletlist)
build_verlet_lists();
calculate_verlet_virials(v_comp);
}
else
calculate_link_cell_virials(v_comp);
break;
case CELL_STRUCTURE_NSQUARE:
nsq_calculate_virials(v_comp);
}
/* rescale kinetic energy (=ideal contribution) */
#ifdef ROTATION_PER_PARTICLE
fprintf(stderr, "Switching rotation per particle (#define ROTATION_PER_PARTICLE) and pressure calculation are incompatible.\n");
#endif
virials.data.e[0] /= (3.0*volume*time_step*time_step);
calc_long_range_virials();
for (n = 1; n < virials.data.n; n++)
virials.data.e[n] /= 3.0*volume;
/* stress tensor part */
/* The ROTATION option does not effect stress tensor calculations
since rotational energy is not included in the ideal term (unlike
for the pressure) */
for(i=0; i<9; i++)
p_tensor.data.e[i] /= (volume*time_step*time_step);
for(i=9; i<p_tensor.data.n; i++)
p_tensor.data.e[i] /= volume;
/* Intra- and Inter- part of nonbonded interaction */
for (n = 0; n < virials_non_bonded.data_nb.n; n++)
virials_non_bonded.data_nb.e[n] /= 3.0*volume;
for(i=0; i<p_tensor_non_bonded.data_nb.n; i++)
p_tensor_non_bonded.data_nb.e[i] /= volume;
/* gather data */
MPI_Reduce(virials.data.e, result, virials.data.n, MPI_DOUBLE, MPI_SUM, 0, comm_cart);
MPI_Reduce(p_tensor.data.e, result_t, p_tensor.data.n, MPI_DOUBLE, MPI_SUM, 0, comm_cart);
MPI_Reduce(virials_non_bonded.data_nb.e, result_nb, virials_non_bonded.data_nb.n, MPI_DOUBLE, MPI_SUM, 0, comm_cart);
MPI_Reduce(p_tensor_non_bonded.data_nb.e, result_t_nb, p_tensor_non_bonded.data_nb.n, MPI_DOUBLE, MPI_SUM, 0, comm_cart);
}
void on_integration_start()
{
char *errtext;
EVENT_TRACE(fprintf(stderr, "%d: on_integration_start\n", this_node));
INTEG_TRACE(fprintf(stderr,"%d: on_integration_start: reinit_thermo = %d, resort_particles=%d\n",
this_node,reinit_thermo,resort_particles));
/********************************************/
/* sanity checks */
/********************************************/
if ( time_step < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext, "{010 time_step not set} ");
}
if ( skin < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{011 skin not set} ");
}
if ( temperature < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{012 thermostat not initialized} ");
}
#ifdef NPT
if (integ_switch == INTEG_METHOD_NPT_ISO) {
if (nptiso.piston <= 0.0) {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt on, but piston mass not set} ");
}
#ifdef ELECTROSTATICS
switch(coulomb.method) {
case COULOMB_NONE: break;
#ifdef P3M
case COULOMB_P3M: break;
#endif /*P3M*/
default: {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt only works with P3M} ");
}
}
#endif /*ELECTROSTATICS*/
#ifdef DIPOLES
switch (coulomb.Dmethod) {
case DIPOLAR_NONE: break;
#ifdef DP3M
case DIPOLAR_P3M: break;
#endif
default: {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"NpT does not work with your dipolar method, please use P3M.");
}
}
#endif /* ifdef DIPOLES */
}
#endif /*NPT*/
if (!check_obs_calc_initialized()) return;
#ifdef LB
if(lattice_switch & LATTICE_LB) {
if (lbpar.agrid <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{098 Lattice Boltzmann agrid not set} ");
}
if (lbpar.tau <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{099 Lattice Boltzmann time step not set} ");
}
if (lbpar.rho <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{100 Lattice Boltzmann fluid density not set} ");
}
if (lbpar.viscosity <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{101 Lattice Boltzmann fluid viscosity not set} ");
}
if (dd.use_vList && skin>=lbpar.agrid/2.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext, "{104 LB requires either no Verlet lists or that the skin of the verlet list to be less than half of lattice-Boltzmann grid spacing.} ");
}
}
#endif
#ifdef LB_GPU
if(this_node == 0){
if(lattice_switch & LATTICE_LB_GPU) {
if (lbpar_gpu.agrid < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{098 Lattice Boltzmann agrid not set} ");
}
if (lbpar_gpu.tau < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{099 Lattice Boltzmann time step not set} ");
}
if (lbpar_gpu.rho < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{100 Lattice Boltzmann fluid density not set} ");
}
if (lbpar_gpu.viscosity < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{101 Lattice Boltzmann fluid viscosity not set} ");
}
if (lb_reinit_particles_gpu) {
lb_realloc_particles_gpu();
lb_reinit_particles_gpu = 0;
}
}
}
#endif
#ifdef METADYNAMICS
meta_init();
#endif
#ifdef CATALYTIC_REACTIONS
if(reaction.ct_rate != 0.0) {
if( dd.use_vList == 0 || cell_structure.type != CELL_STRUCTURE_DOMDEC) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{105 The CATALYTIC_REACTIONS feature requires verlet lists and domain decomposition} ");
check_runtime_errors();
}
if(max_cut < reaction.range) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{106 Reaction range of %f exceeds maximum cutoff of %f} ", reaction.range, max_cut);
}
}
#endif
/********************************************/
/* end sanity checks */
/********************************************/
/* Prepare the thermostat */
if (reinit_thermo) {
thermo_init();
reinit_thermo = 0;
recalc_forces = 1;
}
/* Ensemble preparation: NVT or NPT */
integrate_ensemble_init();
/* Update particle and observable information for routines in statistics.c */
invalidate_obs();
freePartCfg();
on_observable_calc();
}
void on_integration_start()
{
char *errtext;
int i;
EVENT_TRACE(fprintf(stderr, "%d: on_integration_start\n", this_node));
INTEG_TRACE(fprintf(stderr,"%d: on_integration_start: reinit_thermo = %d, resort_particles=%d\n",
this_node,reinit_thermo,resort_particles));
/********************************************/
/* sanity checks */
/********************************************/
if ( time_step < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext, "{010 time_step not set} ");
}
if ( skin < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{011 skin not set} ");
}
if ( temperature < 0.0 ) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{012 thermostat not initialized} ");
}
for (i = 0; i < 3; i++)
if (local_box_l[i] < max_range) {
errtext = runtime_error(128 + TCL_INTEGER_SPACE);
ERROR_SPRINTF(errtext,"{013 box_l in direction %d is still too small} ", i);
}
#ifdef NPT
if (integ_switch == INTEG_METHOD_NPT_ISO) {
if (nptiso.piston <= 0.0) {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt on, but piston mass not set} ");
}
if(cell_structure.type!=CELL_STRUCTURE_DOMDEC) {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt requires domain decomposition cellsystem} ");
}
#ifdef ELECTROSTATICS
switch(coulomb.method) {
case COULOMB_NONE: break;
#ifdef ELP3M
case COULOMB_P3M: break;
#endif /*ELP3M*/
case COULOMB_EWALD: break;
default: {
char *errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{014 npt only works with Ewald sum or P3M} ");
}
}
#endif /*ELECTROSTATICS*/
}
#endif /*NPT*/
if (!check_obs_calc_initialized()) return;
#ifdef LB
if(lattice_switch & LATTICE_LB) {
if (lbpar.agrid <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{098 Lattice Boltzmann agrid not set} ");
}
if (lbpar.tau <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{099 Lattice Boltzmann time step not set} ");
}
if (lbpar.rho <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{100 Lattice Boltzmann fluid density not set} ");
}
if (lbpar.viscosity <= 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{101 Lattice Boltzmann fluid viscosity not set} ");
}
}
#endif
#ifdef LB_GPU
if(this_node == 0){
if(lattice_switch & LATTICE_LB_GPU) {
if (lbpar_gpu.agrid < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{098 Lattice Boltzmann agrid not set} ");
}
if (lbpar_gpu.tau < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{099 Lattice Boltzmann time step not set} ");
}
if (lbpar_gpu.rho < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{100 Lattice Boltzmann fluid density not set} ");
}
if (lbpar_gpu.viscosity < 0.0) {
errtext = runtime_error(128);
ERROR_SPRINTF(errtext,"{101 Lattice Boltzmann fluid viscosity not set} ");
}
if (lb_reinit_particles_gpu) {
lb_realloc_particles_gpu();
lb_reinit_particles_gpu = 0;
}
}
}
#endif
#ifdef METADYNAMICS
meta_init();
#endif
/********************************************/
/* end sanity checks */
/********************************************/
/* Prepare the thermostat */
if (reinit_thermo) {
thermo_init();
reinit_thermo = 0;
recalc_forces = 1;
}
/* Ensemble preparation: NVT or NPT */
integrate_ensemble_init();
/* Update particle and observable information for routines in statistics.c */
invalidate_obs();
freePartCfg();
on_observable_calc();
}
