void update_pressure(int v_comp) {
int i;
double p_vel[3];
/* if desired (v_comp==1) replace ideal component with instantaneous one */
if (total_pressure.init_status != 1+v_comp ) {
init_virials(&total_pressure);
init_p_tensor(&total_p_tensor);
init_virials_non_bonded(&total_pressure_non_bonded);
init_p_tensor_non_bonded(&total_p_tensor_non_bonded);
if(v_comp && (integ_switch == INTEG_METHOD_NPT_ISO) && !(nptiso.invalidate_p_vel)) {
if (total_pressure.init_status == 0)
master_pressure_calc(0);
total_pressure.data.e[0] = 0.0;
MPI_Reduce(nptiso.p_vel, p_vel, 3, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
for(i=0; i<3; i++)
if(nptiso.geometry & nptiso.nptgeom_dir[i])
total_pressure.data.e[0] += p_vel[i];
total_pressure.data.e[0] /= (nptiso.dimension*nptiso.volume);
total_pressure.init_status = 1+v_comp; }
else
master_pressure_calc(v_comp);
}
}
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 (!interactions_sanity_checks())
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();
#ifdef VIRTUAL_SITES_RELATIVE
vs_relative_pressure_and_stress_tensor(virials.vs_relative,p_tensor.vs_relative);
#endif
for (n = 1; n < virials.data.n; n++)
virials.data.e[n] /= 3.0*volume;
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);
}
int tclcommand_analyze_parse_and_print_pressure(Tcl_Interp *interp, int v_comp, int argc, char **argv)
{
/* 'analyze pressure [{ bond <type_num> | nonbonded <type1> <type2> | coulomb | ideal | total }]' */
char buffer[TCL_DOUBLE_SPACE + TCL_INTEGER_SPACE + 2];
int i, j;
double value, p_vel[3];
value = 0.0;
if (n_part == 0) {
Tcl_AppendResult(interp, "(no particles)",
(char *)NULL);
return (TCL_OK);
}
/* if desired (v_comp==1) replace ideal component with instantaneous one */
if (total_pressure.init_status != 1+v_comp ) {
init_virials(&total_pressure);
init_p_tensor(&total_p_tensor);
init_virials_non_bonded(&total_pressure_non_bonded);
init_p_tensor_non_bonded(&total_p_tensor_non_bonded);
if(v_comp && (integ_switch == INTEG_METHOD_NPT_ISO) && !(nptiso.invalidate_p_vel)) {
if (total_pressure.init_status == 0)
master_pressure_calc(0);
total_pressure.data.e[0] = 0.0;
MPI_Reduce(nptiso.p_vel, p_vel, 3, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
for(i=0; i<3; i++)
if(nptiso.geometry & nptiso.nptgeom_dir[i])
total_pressure.data.e[0] += p_vel[i];
total_pressure.data.e[0] /= (nptiso.dimension*nptiso.volume);
total_pressure.init_status = 1+v_comp; }
else
master_pressure_calc(v_comp);
}
if (argc == 0)
tclcommand_analyze_print_pressure_all(interp);
else {
if (ARG0_IS_S("ideal"))
value = total_pressure.data.e[0];
else if (ARG0_IS_S("bonded") ||
ARG0_IS_S("fene") ||
ARG0_IS_S("subt_lj_harm") ||
ARG0_IS_S("subt_lj_fene") ||
ARG0_IS_S("subt_lj") ||
ARG0_IS_S("harmonic") ||
ARG0_IS_S("endangledist")) {
if(argc<2 || ! ARG1_IS_I(i)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze pressure bonded <type_num>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_bonded_ia) {
Tcl_AppendResult(interp, "bond type does not exist", (char *)NULL);
return (TCL_ERROR);
}
value = *obsstat_bonded(&total_pressure, i);
}
else if (ARG0_IS_S("nonbonded") ||
ARG0_IS_S("lj") ||
ARG0_IS_S("buckingham") ||
ARG0_IS_S("morse") ||
ARG0_IS_S("soft-sphere") ||
ARG0_IS_S("lj-cos") ||
ARG0_IS_S("lj-cos2") ||
ARG0_IS_S("tabulated") ||
ARG0_IS_S("gb")) {
if(argc<3 || ! ARG_IS_I(1, i) || ! ARG_IS_I(2, j)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze pressure nonbonded <type1> <type2>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_particle_types || j < 0 || j >= n_particle_types) {
Tcl_AppendResult(interp, "particle type does not exist", (char *)NULL);
return (TCL_ERROR);
}
value = *obsstat_nonbonded(&total_pressure, i, j);
}
else if( ARG0_IS_S("tot_nb_intra") ||
ARG0_IS_S("tot_nonbonded_intra")) {
value = 0.0;
for (i = 0; i < n_particle_types; i++)
for (j = i; j < n_particle_types; j++)
value += *obsstat_nonbonded_intra(&total_pressure_non_bonded, i, j);
}
else if( ARG0_IS_S("tot_nb_inter") ||
ARG0_IS_S("tot_nonbonded_inter")) {
value = 0.0;
for (i = 0; i < n_particle_types; i++)
for (j = i; j < n_particle_types; j++)
value += *obsstat_nonbonded_inter(&total_pressure_non_bonded, i, j);
}
else if( ARG0_IS_S("nb_intra") ||
ARG0_IS_S("nonbonded_intra")) {
if(argc<3 || ! ARG_IS_I(1, i) || ! ARG_IS_I(2, j)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze pressure nb_intra <type1> <type2>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_particle_types || j < 0 || j >= n_particle_types) {
Tcl_AppendResult(interp, "particle type does not exist", (char *)NULL);
return (TCL_ERROR);
}
value = *obsstat_nonbonded_intra(&total_pressure_non_bonded, i, j);
}
else if( ARG0_IS_S("nb_inter") ||
ARG0_IS_S("nonbonded_inter")) {
if(argc<3 || ! ARG_IS_I(1, i) || ! ARG_IS_I(2, j)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze pressure nb_inter <type1> <type2>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_particle_types || j < 0 || j >= n_particle_types) {
Tcl_AppendResult(interp, "particle type does not exist", (char *)NULL);
return (TCL_ERROR);
}
value = *obsstat_nonbonded_inter(&total_pressure_non_bonded, i, j);
}
else if( ARG0_IS_S("coulomb")) {
#ifdef ELECTROSTATICS
value = 0;
for (i = 0; i < total_pressure.n_coulomb; i++)
value += total_pressure.coulomb[i];
#else
Tcl_AppendResult(interp, "ELECTROSTATICS not compiled (see config.hpp)\n", (char *)NULL);
#endif
}
else if( ARG0_IS_S("dipolar")) {
#ifdef DIPOLES
value = 0;
for (i = total_pressure.n_coulomb-1; i < total_pressure.n_coulomb; i++) /*when DLC will be installed this has to be changed */
value += total_pressure.coulomb[i];
#else
Tcl_AppendResult(interp, "DIPOLES not compiled (see config.hpp)\n", (char *)NULL);
#endif
}
#ifdef VIRTUAL_SITES_RELATIVE
else if (ARG0_IS_S("vs_relative")) {
value =total_pressure.vs_relative[0];
}
#endif
else if (ARG0_IS_S("total")) {
value = total_pressure.data.e[0];
for (i = 1; i < total_pressure.data.n; i++) {
value += total_pressure.data.e[i];
}
}
else {
Tcl_AppendResult(interp, "unknown feature of: analyze pressure",
(char *)NULL);
return (TCL_ERROR);
}
Tcl_PrintDouble(interp, value, buffer);
Tcl_AppendResult(interp, buffer, (char *)NULL);
}
return (TCL_OK);
}
int tclcommand_analyze_parse_and_print_stress_tensor(Tcl_Interp *interp, int v_comp, int argc, char **argv)
{
/* 'analyze stress_tensor [{ bond <type_num> | nonbonded <type1> <type2> | coulomb | ideal | total }]' */
char buffer[TCL_DOUBLE_SPACE + TCL_INTEGER_SPACE + 2];
int i, j, k;
double p_vel[3], tvalue[9];
for(j=0; j<9; j++) tvalue[j] = 0.0;
if (n_part == 0) {
Tcl_AppendResult(interp, "(no particles)",
(char *)NULL);
return (TCL_OK);
}
/* if desired (v_comp==1) replace ideal component with instantaneous one */
if (total_pressure.init_status != 1+v_comp ) {
init_virials(&total_pressure);
init_p_tensor(&total_p_tensor);
init_virials_non_bonded(&total_pressure_non_bonded);
init_p_tensor_non_bonded(&total_p_tensor_non_bonded);
if(v_comp && (integ_switch == INTEG_METHOD_NPT_ISO) && !(nptiso.invalidate_p_vel)) {
if (total_pressure.init_status == 0)
master_pressure_calc(0);
p_tensor.data.e[0] = 0.0;
MPI_Reduce(nptiso.p_vel, p_vel, 3, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);
for(i=0; i<3; i++)
if(nptiso.geometry & nptiso.nptgeom_dir[i])
p_tensor.data.e[0] += p_vel[i];
p_tensor.data.e[0] /= (nptiso.dimension*nptiso.volume);
total_pressure.init_status = 1+v_comp; }
else
master_pressure_calc(v_comp);
}
if (argc == 0)
tclcommand_analyze_print_stress_tensor_all(interp);
else {
if (ARG0_IS_S("ideal")) {
for(j=0; j<9; j++) tvalue[j] = total_p_tensor.data.e[j];
}
else if (ARG0_IS_S("bonded") ||
ARG0_IS_S("fene") ||
ARG0_IS_S("subt_lj_harm") ||
ARG0_IS_S("subt_lj_fene") ||
ARG0_IS_S("subt_lj") ||
ARG0_IS_S("harmonic") ||
ARG0_IS_S("endangledist")) {
if(argc<2 || ! ARG1_IS_I(i)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze pressure bonded <type_num>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_bonded_ia) {
Tcl_AppendResult(interp, "bond type does not exist", (char *)NULL);
return (TCL_ERROR);
}
for(k=0; k<9; k++) tvalue[k] = obsstat_bonded(&total_p_tensor, i)[k];
}
else if (ARG0_IS_S("nonbonded") ||
ARG0_IS_S("lj") ||
ARG0_IS_S("buckingham") ||
ARG0_IS_S("morse") ||
ARG0_IS_S("soft-sphere") ||
ARG0_IS_S("lj-cos") ||
ARG0_IS_S("lj-cos2") ||
ARG0_IS_S("tabulated") ||
ARG0_IS_S("gb")) {
if(argc<3 || ! ARG_IS_I(1, i) || ! ARG_IS_I(2, j)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze pressure nonbonded <type1> <type2>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_particle_types || j < 0 || j >= n_particle_types) {
Tcl_AppendResult(interp, "particle type does not exist", (char *)NULL);
return (TCL_ERROR);
}
for(k=0; k<9; k++) tvalue[k] = obsstat_nonbonded(&total_p_tensor, i, j)[k];
}
else if( ARG0_IS_S("tot_nb_intra")) {
for(k=0; k<9; k++) {
for (i = 0; i < n_particle_types; i++)
for (j = i; j < n_particle_types; j++) {
tvalue[k] += obsstat_nonbonded_intra(&total_p_tensor_non_bonded, i, j)[k];
}
}
}
else if( ARG0_IS_S("tot_nb_inter")) {
for(k=0; k<9; k++) {
for (i = 0; i < n_particle_types; i++)
for (j = i; j < n_particle_types; j++) {
tvalue[k] += obsstat_nonbonded_inter(&total_p_tensor_non_bonded, i, j)[k];
}
}
}
else if( ARG0_IS_S("nb_intra")) {
if(argc<3 || ! ARG_IS_I(1, i) || ! ARG_IS_I(2, j)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze stress tensor nonbonded <type1> <type2>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_particle_types || j < 0 || j >= n_particle_types) {
Tcl_AppendResult(interp, "particle type does not exist", (char *)NULL);
return (TCL_ERROR);
}
for(k=0; k<9; k++) tvalue[k] = obsstat_nonbonded_intra(&total_p_tensor_non_bonded, i, j)[k];
}
else if( ARG0_IS_S("nb_inter")) {
if(argc<3 || ! ARG_IS_I(1, i) || ! ARG_IS_I(2, j)) {
Tcl_ResetResult(interp);
Tcl_AppendResult(interp, "wrong # or type of arguments for: analyze stress tensor nonbonded <type1> <type2>",
(char *)NULL);
return (TCL_ERROR);
}
if(i < 0 || i >= n_particle_types || j < 0 || j >= n_particle_types) {
Tcl_AppendResult(interp, "particle type does not exist", (char *)NULL);
return (TCL_ERROR);
}
for(k=0; k<9; k++) tvalue[k] = obsstat_nonbonded_inter(&total_p_tensor_non_bonded, i, j)[k];
}
else if( ARG0_IS_S("coulomb")) {
#ifdef ELECTROSTATICS
for(j=0; j<9; j++) tvalue[j] = total_p_tensor.coulomb[j];
#else
Tcl_AppendResult(interp, "ELECTROSTATICS not compiled (see config.hpp)\n", (char *)NULL);
#endif
}
else if( ARG0_IS_S("dipolar")) {
#ifdef DIPOLES
/* for(j=0; j<9; j++) tvalue[j] = total_p_tensor.coulomb[j];*/
fprintf(stderr," stress tensor, magnetostatics, something should go here, file pressure.cpp ");
#else
Tcl_AppendResult(interp, "DIPOLES not compiled (see config.hpp)\n", (char *)NULL);
#endif
}
#ifdef VIRTUAL_SITES_RELATIVE
else if (ARG0_IS_S("VS_RELATIVE")) {
for(j=0; j<9; j++) tvalue[j] = total_p_tensor.vs_relative[j];
}
#endif
else if (ARG0_IS_S("total")) {
for(j=0; j<9; j++) {
tvalue[j] = total_p_tensor.data.e[j];
for (i = 1; i < total_p_tensor.data.n/9; i++) tvalue[j] += total_p_tensor.data.e[9*i + j];
}
}
else {
Tcl_AppendResult(interp, "unknown feature of: analyze pressure",
(char *)NULL);
return (TCL_ERROR);
}
Tcl_AppendResult(interp, *argv, (char *)NULL);
Tcl_AppendResult(interp, " ", (char *)NULL);
for(j=0; j<9; j++) {
Tcl_PrintDouble(interp, tvalue[j], buffer);
Tcl_AppendResult(interp, buffer, " ", (char *)NULL);
}
}
return (TCL_OK);
}
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) */
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 */
/* 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);
}
