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); }