--- trunk/src/io/Globals.cpp 2005/09/16 16:07:39 603 +++ trunk/src/io/Globals.cpp 2008/09/11 19:40:59 1291 @@ -42,2034 +42,189 @@ #include #include #include - -#include "io/Globals.hpp" -#include "utils/simError.h" -#ifdef IS_MPI -#include "io/mpiBASS.h" -#endif // is_mpi - -/* - * The following section lists all of the defined tokens for the - * global assignment statements. All are prefixed with a G_ to avoid - * stepping on any previously defined enumerations. - * - * NOTE: tokens start at 1, 0 is a resrved token number - */ - -//required parameters -#define G_FORCEFIELD 1 -#define G_NCOMPONENTS 2 -#define G_TARGETTEMP 3 -#define G_ENSEMBLE 4 -#define G_DT 5 -#define G_RUNTIME 6 - -//optional parameters -#define G_INITIALCONFIG 7 -#define G_FINALCONFIG 8 -#define G_NMOL 9 -#define G_DENSITY 10 -#define G_BOX 11 -#define G_BOXX 12 -#define G_BOXY 13 -#define G_BOXZ 14 -#define G_SAMPLETIME 15 -#define G_STATUSTIME 16 -#define G_RCUT 17 -#define G_RSW 18 -#define G_DIELECTRIC 19 -#define G_TEMPSET 20 -#define G_THERMALTIME 21 -#define G_USEPBC 22 -#define G_MIXINGRULE 23 -#define G_TARGETPRESSURE 24 -#define G_TAUTHERMOSTAT 25 -#define G_TAUBAROSTAT 26 -#define G_ZCONSTIME 27 -#define G_NZCONSTRAINTS 28 -#define G_ZCONSTOL 29 -#define G_ZCONSFORCEPOLICY 30 -#define G_SEED 31 -#define G_RESETTIME 32 -#define G_USEINITTIME 33 -#define G_USEINIT_XS_STATE 34 -#define G_ORTHOBOXTOLERANCE 35 -#define G_MINIMIZER 36 -#define G_MIN_MAXITER 37 -#define G_MIN_WRITEFRQ 38 -#define G_MIN_STEPSIZE 39 -#define G_MIN_FTOL 40 -#define G_MIN_GTOL 41 -#define G_MIN_LSTOL 42 -#define G_MIN_LSMAXITER 43 -#define G_ZCONSGAP 44 -#define G_ZCONSFIXTIME 45 -#define G_ZCONSUSINGSMD 46 -#define G_USE_SOLID_THERM_INT 47 -#define G_USE_LIQUID_THERM_INT 48 -#define G_THERM_INT_LAMBDA 49 -#define G_THERM_INT_K 50 -#define G_FORCEFIELD_VARIANT 51 -#define G_FORCEFIELD_FILENAME 52 -#define G_THERM_INT_DIST_SPRING 53 -#define G_THERM_INT_THETA_SPRING 54 -#define G_THERM_INT_OMEGA_SPRING 55 -#define G_SURFACETENSION 56 -#define G_PRINTPRESSURETENSOR 57 -#define G_ELECTRO_SUM_METHOD 58 -#define G_DAMPING_ALPHA 59 -#define G_CUTOFFPOLICY 60 - -Globals::Globals(){ - initalize(); -} - -Globals::~Globals(){ - int i; - if( components != NULL ){ - for( i=0; ievt.blk_index; - char err[200]; - - if( have_n_components && index < n_components ) - components[index] = current_component; - else{ - if( have_n_components ){ - sprintf( err, "meta-data parsing error: %d out of nComponents range", - index ); - the_event->err_msg = strdup( err ); - return 0; - } - else{ - the_event->err_msg = strdup("meta-data parsing error: nComponents not given before" - " first component declaration." ); - return 0; - } - } - - return 1; -} - - - -int Globals::componentAssign( event* the_event ){ - - switch( the_event->evt.asmt.asmt_type ){ - - case STRING: - return current_component->assignString( the_event->evt.asmt.lhs, - the_event->evt.asmt.rhs.sval, - &(the_event->err_msg)); - break; - - case DOUBLE: - return current_component->assignDouble( the_event->evt.asmt.lhs, - the_event->evt.asmt.rhs.dval, - &(the_event->err_msg)); - break; - - case INT: - return current_component->assignInt( the_event->evt.asmt.lhs, - the_event->evt.asmt.rhs.ival, - &(the_event->err_msg)); - break; - - default: - the_event->err_msg = strdup( "Globals error. Invalid component" - " assignment type" ); - return 0; - break; - } - return 0; -} - -int Globals::componentEnd( event* the_event ){ - - the_event->err_msg = current_component->checkMe(); - if( the_event->err_msg != NULL ) return 0; - - return 1; -} - -int Globals::newZconstraint( event* the_event ){ - - - int index = the_event->evt.blk_index; - char err[200]; - current_zConstraint = new ZconStamp( index ); - - have_zConstraints = 1; - - if( have_n_zConstraints && index < n_zConstraints ) - zConstraints[index] = current_zConstraint; - else{ - if( have_n_zConstraints ){ - sprintf( err, "meta-data parsing error: %d out of nZconstraints range", - index ); - the_event->err_msg = strdup( err ); - return 0; - } - else{ - the_event->err_msg = strdup("meta-data parsing error: nZconstraints" - " not given before" - " first zConstraint declaration." ); - return 0; - } - } - - return 1; -} - - - -int Globals::zConstraintAssign( event* the_event ){ - - switch( the_event->evt.asmt.asmt_type ){ - - case STRING: - return current_zConstraint->assignString( the_event->evt.asmt.lhs, - the_event->evt.asmt.rhs.sval, - &(the_event->err_msg)); - break; - - case DOUBLE: - return current_zConstraint->assignDouble( the_event->evt.asmt.lhs, - the_event->evt.asmt.rhs.dval, - &(the_event->err_msg)); - break; - - case INT: - return current_zConstraint->assignInt( the_event->evt.asmt.lhs, - the_event->evt.asmt.rhs.ival, - &(the_event->err_msg)); - break; - - default: - the_event->err_msg = strdup( "Globals error. Invalid zConstraint" - " assignment type" ); - return 0; - break; - } - return 0; -} - -int Globals::zConstraintEnd( event* the_event ){ - - the_event->err_msg = current_zConstraint->checkMe(); - if( the_event->err_msg != NULL ) return 0; - - return 1; -} - -int Globals::globalAssign( event* the_event ){ - - int key; - int token; - interface_assign_type the_type = the_event->evt.asmt.asmt_type; - char* lhs = the_event->evt.asmt.lhs; - char err[300]; - - token = 0; - - CommandMapType::iterator iter; - std::string keyword(lhs); - iter = command_table.find(keyword); - if (iter != command_table.end()) { - token = iter->second; - } - - if( token ){ - - switch( token ){ - - case G_FORCEFIELD: - if( the_type == STRING ){ - strcpy( force_field, the_event->evt.asmt.rhs.sval ); - have_force_field = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tforceField was not a string assignment.\n" ); - return 0; - break; - - case G_NCOMPONENTS: - if( the_type == STRING ){ - the_event->err_msg = - strdup("Error in parsing meta-data file!\n\tnComponents is not a double or an int.\n" ); - return 0; - } - - else if( the_type == DOUBLE ){ - n_components = (int)the_event->evt.asmt.rhs.dval; - components = new Component*[n_components]; - have_n_components = 1; - return 1; - } - - else{ - n_components = the_event->evt.asmt.rhs.ival; - components = new Component*[n_components]; - have_n_components = 1; - return 1; - } - break; - - case G_NZCONSTRAINTS: - if( the_type == STRING ){ - the_event->err_msg = - strdup("Error in parsing meta-data file!\n\tnZconstraints is not a double or an int.\n" ); - return 0; - } - - else if( the_type == DOUBLE ){ - n_zConstraints = (int)the_event->evt.asmt.rhs.dval; - zConstraints = new ZconStamp*[n_zConstraints]; - have_n_zConstraints = 1; - return 1; - } - - else{ - n_zConstraints = the_event->evt.asmt.rhs.ival; - zConstraints = new ZconStamp*[n_zConstraints]; - have_n_zConstraints = 1; - return 1; - } - break; - - case G_TARGETTEMP: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttargetTemp is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - target_temp = the_event->evt.asmt.rhs.dval; - have_target_temp = 1; - return 1; - break; - - case INT: - target_temp = (double)the_event->evt.asmt.rhs.ival; - have_target_temp = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttargetTemp unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ORTHOBOXTOLERANCE: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\torthoBoxTolerance is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - orthoBoxTolerance = the_event->evt.asmt.rhs.dval; - have_target_temp = 1; - return 1; - break; - - case INT: - orthoBoxTolerance = (double)the_event->evt.asmt.rhs.ival; - have_target_temp = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Global error.orthoBoxTolerance unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ENSEMBLE: - if( the_type == STRING ){ - strcpy( ensemble, the_event->evt.asmt.rhs.sval ); - have_ensemble = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tensemble was not assigned to a string\n" ); - return 0; - break; - - case G_MIXINGRULE: - if( the_type == STRING ){ - strcpy( mixingRule, the_event->evt.asmt.rhs.sval ); - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tmixing rule was not assigned to a string\n" ); - return 0; - break; - - case G_DT: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdt is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - dt = the_event->evt.asmt.rhs.dval; - have_dt = 1; - return 1; - break; - - case INT: - dt = (double)the_event->evt.asmt.rhs.ival; - have_dt = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdt unrecognized.\n" ); - return 0; - break; - } - break; - - case G_RUNTIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\trunTime is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - run_time = the_event->evt.asmt.rhs.dval; - have_run_time = 1; - return 1; - break; - - case INT: - run_time = (double)the_event->evt.asmt.rhs.ival; - have_run_time = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\trunTime unrecognized.\n" ); - return 0; - break; - } - break; - - case G_INITIALCONFIG: - if( the_type == STRING ){ - strcpy( initial_config, the_event->evt.asmt.rhs.sval ); - have_initial_config = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tinitialConfig was not a string assignment.\n" ); - return 0; - break; - - case G_FINALCONFIG: - if( the_type == STRING ){ - strcpy( final_config, the_event->evt.asmt.rhs.sval ); - have_final_config = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tfinalConfig was not a string assignment.\n" ); - return 0; - break; - - case G_NMOL: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tnMol is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - n_mol = (int)the_event->evt.asmt.rhs.dval; - have_n_mol = 1; - return 1; - break; - - case INT: - n_mol = the_event->evt.asmt.rhs.ival; - have_n_mol = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tnMol unrecognized.\n" ); - return 0; - break; - } - break; - - case G_DENSITY: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdensity is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - density = the_event->evt.asmt.rhs.dval; - have_density = 1; - return 1; - break; - - case INT: - density = (double)the_event->evt.asmt.rhs.ival; - have_density = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdensity unrecognized.\n" ); - return 0; - break; - } - break; - - case G_BOX: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tbox is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - box = the_event->evt.asmt.rhs.dval; - have_box = 1; - return 1; - break; - - case INT: - box = (double)the_event->evt.asmt.rhs.ival; - have_box = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tbox unrecognized.\n" ); - return 0; - break; - } - break; - - case G_BOXX: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tboxX is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - box_x = the_event->evt.asmt.rhs.dval; - have_box_x = 1; - return 1; - break; - - case INT: - box_x = (double)the_event->evt.asmt.rhs.ival; - have_box_x = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tboxX unrecognized.\n" ); - return 0; - break; - } - break; - - case G_BOXY: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tboxY is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - box_y = the_event->evt.asmt.rhs.dval; - have_box_y = 1; - return 1; - break; - - case INT: - box_y = (double)the_event->evt.asmt.rhs.ival; - have_box_y = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tboxY unrecognized.\n" ); - return 0; - break; - } - break; - - case G_BOXZ: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tboxZ is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - box_z = the_event->evt.asmt.rhs.dval; - have_box_z = 1; - return 1; - break; - - case INT: - box_z = (double)the_event->evt.asmt.rhs.ival; - have_box_z = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tboxZ unrecognized.\n" ); - return 0; - break; - } - break; - - case G_SAMPLETIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tsampleTime is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - sample_time = the_event->evt.asmt.rhs.dval; - have_sample_time = 1; - return 1; - break; - - case INT: - sample_time = (double)the_event->evt.asmt.rhs.ival; - have_sample_time = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tsampleTime unrecognized.\n" ); - return 0; - break; - } - break; - - case G_STATUSTIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tstatusTime is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - status_time = the_event->evt.asmt.rhs.dval; - have_status_time = 1; - return 1; - break; - - case INT: - status_time = (double)the_event->evt.asmt.rhs.ival; - have_status_time = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tstatusTime unrecognized.\n" ); - return 0; - break; - } - break; - - case G_RESETTIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tresetTime is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - resetTime = the_event->evt.asmt.rhs.dval; - have_reset_time = 1; - return 1; - break; - - case INT: - resetTime = (double)the_event->evt.asmt.rhs.ival; - have_reset_time = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tresetTime unrecognized.\n" ); - return 0; - break; - } - break; - - case G_THERMALTIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - thermal_time = the_event->evt.asmt.rhs.dval; - have_thermal_time = 1; - return 1; - break; - - case INT: - thermal_time = (double)the_event->evt.asmt.rhs.ival; - have_thermal_time = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermalTime unrecognized.\n" ); - return 0; - break; - } - break; - - case G_RCUT: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tcutoffRadius is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - rcut = the_event->evt.asmt.rhs.dval; - have_rcut = 1; - return 1; - break; - - case INT: - rcut = (double)the_event->evt.asmt.rhs.ival; - have_rcut = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tcutoffRadius unrecognized.\n" ); - return 0; - break; - } - break; - - case G_RSW: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tswitchingRadius is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - rsw = the_event->evt.asmt.rhs.dval; - have_rsw = 1; - return 1; - break; - - case INT: - rsw = (double)the_event->evt.asmt.rhs.ival; - have_rsw = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" ); - return 0; - break; - } - break; - - case G_DIELECTRIC: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdielectric is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - dielectric = the_event->evt.asmt.rhs.dval; - have_dielectric = 1; - return 1; - break; - - case INT: - dielectric = (double)the_event->evt.asmt.rhs.ival; - have_dielectric = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdielectric unrecognized.\n" ); - return 0; - break; - } - break; - - case G_TEMPSET: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) tempSet = 1; - else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) tempSet = 0; - else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" ); - return 0; - } - have_tempSet = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_USEINITTIME: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useInitTime = 1; - else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useInitTime = 0; - else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" ); - return 0; - } - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_USEINIT_XS_STATE: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) - useInitXSstate = 1; - else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) - useInitXSstate = 0; - else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" ); - return 0; - } - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_USEPBC: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) usePBC = 1; - else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) usePBC = 0; - else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" ); - return 0; - } - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_TARGETPRESSURE: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttargetPressure is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - target_pressure = the_event->evt.asmt.rhs.dval; - have_target_pressure = 1; - return 1; - break; - - case INT: - target_pressure = (double)the_event->evt.asmt.rhs.ival; - have_target_pressure = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttargetPressure unrecognized.\n" ); - return 0; - break; - } - break; - - case G_TAUTHERMOSTAT: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttauThermostat is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - tau_thermostat = the_event->evt.asmt.rhs.dval; - have_tau_thermostat = 1; - return 1; - break; - - case INT: - tau_thermostat = (double)the_event->evt.asmt.rhs.ival; - have_tau_thermostat = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttauThermostat unrecognized.\n" ); - return 0; - break; - } - break; - - case G_TAUBAROSTAT: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttauBarostat is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - tau_barostat = the_event->evt.asmt.rhs.dval; - have_tau_barostat = 1; - return 1; - break; - - case INT: - tau_barostat = (double)the_event->evt.asmt.rhs.ival; - have_tau_barostat = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\ttauBarostat unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ZCONSTIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_time is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - zcons_time = the_event->evt.asmt.rhs.dval; - have_zcons_time = 1; - return 1; - break; - - case INT: - zcons_time = (double)the_event->evt.asmt.rhs.ival; - have_zcons_time = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_time unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ZCONSTOL: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_tol is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - zcons_tol = the_event->evt.asmt.rhs.dval; - have_zcons_tol = 1; - return 1; - break; - - case INT: - zcons_tol = (double)the_event->evt.asmt.rhs.ival; - have_zcons_tol = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_ol unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ZCONSFORCEPOLICY: - switch( the_type ){ - - case STRING: - strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval); - - for(int i = 0; zconsForcePolicy[i] != '\0'; i++) - { - zconsForcePolicy[i] = toupper(zconsForcePolicy[i]); - } - have_zcons_force_policy = 1; - return 1; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" ); - return 0; - break; - - case INT: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" ); - return 0; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ZCONSGAP: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_gap is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - zcons_gap = the_event->evt.asmt.rhs.dval; - have_zcons_gap= 1; - return 1; - break; - - case INT: - zcons_gap= (double)the_event->evt.asmt.rhs.ival; - have_zcons_gap= 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_gap unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ZCONSFIXTIME: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not a double or int.\n" ); - return 0; - break; - - case DOUBLE: - zcons_fixtime= the_event->evt.asmt.rhs.dval; - have_zcons_fixtime= 1; - return 1; - break; - - case INT: - zcons_fixtime= (double)the_event->evt.asmt.rhs.ival; - have_zcons_fixtime= 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_fixtime unrecognized.\n" ); - return 0; - break; - } - break; - - case G_ZCONSUSINGSMD: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an int.\n" ); - return 0; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an int.\n" ); - return 0; - break; - - case INT: - zcons_using_smd= the_event->evt.asmt.rhs.ival; - have_zcons_using_smd= 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tzcons_usingsmd unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MINIMIZER: - switch( the_type ){ - - case STRING: - strcpy(minimizer_name, the_event->evt.asmt.rhs.sval); - - for(int i = 0; zconsForcePolicy[i] != '\0'; i++){ - zconsForcePolicy[i] = toupper(zconsForcePolicy[i]); - } - have_minimizer= 1; - return 1; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" ); - return 0; - break; - - case INT: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" ); - return 0; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_name unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_MAXITER: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - minimizer_maxiteration = (int)the_event->evt.asmt.rhs.dval; - have_minimizer_maxiteration = 1; - return 1; - break; - - case INT: - minimizer_maxiteration = the_event->evt.asmt.rhs.ival; - have_minimizer_maxiteration = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_WRITEFRQ: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" ); - return 1; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" ); - return 1; - break; - - case INT: - minimizer_writefrq= the_event->evt.asmt.rhs.ival; - have_minimizer_writefrq = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_STEPSIZE: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - minimizer_stepsize= the_event->evt.asmt.rhs.dval; - have_minimizer_stepsize = 1; - return 1; - break; - - case INT: - minimizer_stepsize= the_event->evt.asmt.rhs.ival; - have_minimizer_stepsize = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_FTOL: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ftol is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - minimizer_ftol= the_event->evt.asmt.rhs.dval; - have_minimizer_ftol = 1; - return 1; - break; - - case INT: - minimizer_ftol= the_event->evt.asmt.rhs.ival; - have_minimizer_ftol = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ftol unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_GTOL: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_gtol is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - minimizer_gtol= the_event->evt.asmt.rhs.dval; - have_minimizer_gtol = 1; - return 1; - break; - - case INT: - minimizer_gtol= the_event->evt.asmt.rhs.ival; - have_minimizer_gtol = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_gtol unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_LSMAXITER: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" ); - return 1; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" ); - return 1; - break; - - case INT: - minimizer_ls_maxiteration = the_event->evt.asmt.rhs.ival; - have_minimizer_ls_maxiteration = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration unrecognized.\n" ); - return 0; - break; - } - break; - - case G_MIN_LSTOL: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - minimizer_ls_tol= the_event->evt.asmt.rhs.dval; - have_minimizer_ls_tol = 1; - return 1; - break; - - case INT: - minimizer_ls_tol= the_event->evt.asmt.rhs.ival; - have_minimizer_ls_tol = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol unrecognized.\n" ); - return 0; - break; - } - break; - - // add more token cases here. - case G_SEED: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" ); - return 0; - return 0; - break; - - case DOUBLE: - have_seed = 1; - seed = (int)the_event->evt.asmt.rhs.dval; - return 1; - break; - - case INT: - have_seed = 1; - seed = the_event->evt.asmt.rhs.ival ; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tseed unrecognized.\n" ); - return 0; - break; - } - break; - - case G_USE_SOLID_THERM_INT: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 1; - else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 0; - else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" ); - return 0; - } - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_USE_LIQUID_THERM_INT: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 1; - else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 0; - else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" ); - return 0; - } - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_THERM_INT_LAMBDA: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - thermodynamic_integration_lambda = the_event->evt.asmt.rhs.dval; - have_thermodynamic_integration_lambda = 1; - return 1; - break; - - case INT: - thermodynamic_integration_lambda = (double)the_event->evt.asmt.rhs.dval; - have_thermodynamic_integration_lambda = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda unrecognized.\n" ); - return 0; - break; - } - break; - - case G_THERM_INT_K: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - thermodynamic_integration_k = the_event->evt.asmt.rhs.dval; - have_thermodynamic_integration_k = 1; - return 1; - break; - - case INT: - thermodynamic_integration_k = (double)the_event->evt.asmt.rhs.dval; - have_thermodynamic_integration_k = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK unrecognized.\n" ); - return 0; - break; - } - break; - - case G_FORCEFIELD_VARIANT: - if( the_type == STRING ){ - strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval ); - have_forcefield_variant = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" ); - return 0; - break; - // add more token cases here. - - case G_FORCEFIELD_FILENAME: - if( the_type == STRING ){ - strcpy( forcefield_filename, the_event->evt.asmt.rhs.sval ); - have_forcefield_filename = 1; - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tforceFieldFileName was not a string assignment.\n" ); - return 0; - break; - - case G_THERM_INT_DIST_SPRING: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - therm_int_dist_spring = the_event->evt.asmt.rhs.dval; - have_dist_spring_constant = 1; - return 1; - break; - - case INT: - therm_int_dist_spring = (double)the_event->evt.asmt.rhs.dval; - have_dist_spring_constant = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst unrecognized.\n" ); - return 0; - break; - } - break; - - case G_THERM_INT_THETA_SPRING: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - therm_int_theta_spring = the_event->evt.asmt.rhs.dval; - have_theta_spring_constant = 1; - return 1; - break; - - case INT: - therm_int_theta_spring = (double)the_event->evt.asmt.rhs.dval; - have_theta_spring_constant = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst unrecognized.\n" ); - return 0; - break; - } - break; - - case G_THERM_INT_OMEGA_SPRING: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - therm_int_omega_spring = the_event->evt.asmt.rhs.dval; - have_omega_spring_constant = 1; - return 1; - break; - - case INT: - therm_int_omega_spring = (double)the_event->evt.asmt.rhs.dval; - have_omega_spring_constant = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst unrecognized.\n" ); - return 0; - break; - } - break; - - case G_SURFACETENSION: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tsurfaceTension is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - surface_tension= the_event->evt.asmt.rhs.dval; - have_surface_tension = 1; - return 1; - break; - - case INT: - surface_tension = (double)the_event->evt.asmt.rhs.dval; - have_surface_tension = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tsurfaceTension unrecognized.\n" ); - return 0; - break; - } - break; - - case G_PRINTPRESSURETENSOR: - if( the_type == STRING ){ - - if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) { - have_print_pressure_tensor= 1; - print_pressure_tensor = 1; - } else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) { - have_print_pressure_tensor= 1; - print_pressure_tensor = 0; - } else{ - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tprintPressureTensor was not \"true\" or \"false\".\n" ); - return 0; - } - return 1; - } - - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tprintPressureTensor was not \"true\" or \"false\".\n" ); - return 0; - break; - - case G_ELECTRO_SUM_METHOD: - switch( the_type ){ - - case STRING: - strcpy(electrostaticSummationMethod, the_event->evt.asmt.rhs.sval); - - for(int i = 0; electrostaticSummationMethod[i] != '\0'; i++) - { - electrostaticSummationMethod[i] = toupper(electrostaticSummationMethod[i]); - } - have_electro_sum_method = 1; - return 1; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod should be a string!\n" ); - return 0; - break; - - case INT: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod should be a string!\n" ); - return 0; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\telectrostaticSummationMethod unrecognized.\n" ); - return 0; - break; - } - break; - - case G_DAMPING_ALPHA: - switch( the_type ){ - - case STRING: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdampingAlpha is not a double or int.\n" ); - return 1; - break; - - case DOUBLE: - dampingAlpha = the_event->evt.asmt.rhs.dval; - have_damping_alpha = 1; - return 1; - break; - - case INT: - dampingAlpha = (double)the_event->evt.asmt.rhs.dval; - have_damping_alpha = 1; - return 1; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tdampingAlpha unrecognized.\n" ); - return 0; - break; - } - break; - - case G_CUTOFFPOLICY: - switch( the_type ){ - - case STRING: - strcpy(cutoffPolicy, the_event->evt.asmt.rhs.sval); - - for(int i = 0; cutoffPolicy[i] != '\0'; i++) - { - cutoffPolicy[i] = toupper(cutoffPolicy[i]); - } - have_cutoff_policy = 1; - return 1; - break; - - case DOUBLE: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tcutoffPolicy should be a string!\n" ); - return 0; - break; - - case INT: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tcutoffPolicy should be a string!\n" ); - return 0; - break; - - default: - the_event->err_msg = - strdup( "Error in parsing meta-data file!\n\tcutoffPolicy unrecognized.\n" ); - return 0; - break; - } - break; - - - // add more token cases here. - } - } - - switch( the_type ){ - - case STRING: - sprintf( err, - "\tUnrecognized assignment:\n" - "\t\t-> %s = %s\n", - lhs, the_event->evt.asmt.rhs.sval ); - break; - - case DOUBLE: - sprintf( err, - "\tUnrecognized assignment:\n" - "\t\t-> %s = %lf\n", - lhs, the_event->evt.asmt.rhs.dval ); - break; - - case INT: - sprintf( err, - "\tUnrecognized assignment:\n" - "\t\t-> %s = %d\n", - lhs, the_event->evt.asmt.rhs.ival ); - break; - - default: - sprintf( err, - "\tUnrecognized assignment:\n" - "\t\t-> %s = ?\n", - lhs ); - break; - } - - the_event->err_msg = strdup( err ); - return 0; -} - -char* Globals::checkMe( void ){ - - char err[300]; - short int have_err = 0; - - strcpy( err, "The following required keywords are missing:\n" ); - - if( !have_force_field ){ - strcat( err, "\t\t->forceField\n" ); - have_err= 1; - } - - if( !have_n_components ){ - strcat( err, "\t\t->nComponents\n" ); - have_err= 1; - } - - - if ( !have_ensemble ) { - // I'm not doing MD: - if ( !have_minimizer ) { - // I'm not doing MD or minimization: - strcat( err, "\t\t->either ensemble or minimizer must be set!\n" ); - have_err = 1; - } else { - // I'm a minimizer: - } - } else { - // I *am* doing MD: - if( !have_dt ){ - strcat( err, "\t\t->dt (timestep in fs)\n" ); - have_err= 1; - } - if( !have_run_time ){ - strcat( err, "\t\t->runTime (total run time in fs)\n" ); - have_err= 1; - } - } - - if( have_err ) return strdup( err ); - - return NULL; -} - -int Globals::globalEnd( event* the_event ){ - - the_event->err_msg = checkMe(); - if( the_event->err_msg != NULL ) return 0; - - return 1; -} - +#include + +#include "io/Globals.hpp" +#include "io/ParamConstraint.hpp" +#include "utils/MemoryUtils.hpp" +#include "utils/simError.h" + +namespace oopse { +Globals::Globals() { + DefineParameter(ForceField, "forceField") + + DefineOptionalParameter(TargetTemp, "targetTemp"); + DefineOptionalParameter(Ensemble, "ensemble"); + DefineOptionalParameter(Dt, "dt"); + DefineOptionalParameter(RunTime, "runTime"); + DefineOptionalParameter(FinalConfig, "finalConfig"); + DefineOptionalParameter(SampleTime, "sampleTime"); + DefineOptionalParameter(ResetTime, "resetTime"); + DefineOptionalParameter(StatusTime, "statusTime"); + DefineOptionalParameter(CutoffRadius, "cutoffRadius"); + DefineOptionalParameter(SwitchingRadius, "switchingRadius"); + DefineOptionalParameter(TempSet, "tempSet"); + DefineOptionalParameter(ThermalTime, "thermalTime"); + DefineOptionalParameter(TargetPressure, "targetPressure"); + DefineOptionalParameter(TauThermostat, "tauThermostat"); + DefineOptionalParameter(TauBarostat, "tauBarostat"); + DefineOptionalParameter(ZconsTime, "zconsTime"); + DefineOptionalParameter(ZconsTol, "zconsTol"); + DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy"); + DefineOptionalParameter(Seed, "seed"); + DefineOptionalParameter(Minimizer, "minimizer"); + DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); + DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); + DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); + DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); + DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); + DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol"); + DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter"); + DefineOptionalParameter(ZconsGap, "zconsGap"); + DefineOptionalParameter(ZconsFixtime, "zconsFixtime"); + DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD"); + DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda"); + DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK"); + DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); + DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); + DefineOptionalParameter(DampingAlpha, "dampingAlpha"); + DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst"); + DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst"); + DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst"); + DefineOptionalParameter(SurfaceTension, "surfaceTension"); + DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); + DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); + DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); + DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); + DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); + DefineOptionalParameter(HydroPropFile, "HydroPropFile"); + DefineOptionalParameter(Viscosity, "viscosity"); + DefineOptionalParameter(BeadSize, "beadSize"); + DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); + DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); + DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); + + + DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); + DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true); + DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); + DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); + DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); + DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false); + DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false); + DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0); + DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5); + DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5); + DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE"); + DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); + DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5); + DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); + DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); + DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); + DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); + DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); + DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); + + deprecatedKeywords_.insert("nComponents"); + deprecatedKeywords_.insert("nZconstraints"); + deprecatedKeywords_.insert("initialConfig"); + +} + +Globals::~Globals() { + MemoryUtils::deletePointers(components_); + MemoryUtils::deletePointers(zconstraints_); +} + +void Globals::validate() { + DataHolder::validate(); + + CheckParameter(ForceField, isNotEmpty()); + CheckParameter(TargetTemp, isPositive()); + CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT")); + CheckParameter(Dt, isPositive()); + CheckParameter(RunTime, isPositive()); + CheckParameter(FinalConfig, isNotEmpty()); + CheckParameter(SampleTime, isNonNegative()); + CheckParameter(ResetTime, isNonNegative()); + CheckParameter(StatusTime, isNonNegative()); + CheckParameter(CutoffRadius, isPositive()); + CheckParameter(SwitchingRadius, isNonNegative()); + CheckParameter(Dielectric, isPositive()); + CheckParameter(ThermalTime, isNonNegative()); + CheckParameter(TauThermostat, isPositive()); + CheckParameter(TauBarostat, isPositive()); + CheckParameter(ZconsTime, isPositive()); + CheckParameter(ZconsTol, isPositive()); + CheckParameter(Seed, isPositive()); + CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); + CheckParameter(MinimizerMaxIter, isPositive()); + CheckParameter(MinimizerWriteFrq, isPositive()); + CheckParameter(MinimizerStepSize, isPositive()); + CheckParameter(MinimizerFTol, isPositive()); + CheckParameter(MinimizerGTol, isPositive()); + CheckParameter(MinimizerLSTol, isPositive()); + CheckParameter(MinimizerLSMaxIter, isPositive()); + CheckParameter(ZconsGap, isPositive()); + CheckParameter(ZconsFixtime, isPositive()); + CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); + CheckParameter(ThermodynamicIntegrationK, isPositive()); + CheckParameter(ForceFieldVariant, isNotEmpty()); + CheckParameter(ForceFieldFileName, isNotEmpty()); + CheckParameter(ThermIntDistSpringConst, isPositive()); + CheckParameter(ThermIntThetaSpringConst, isPositive()); + CheckParameter(ThermIntOmegaSpringConst, isPositive()); + CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); + CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); + CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL")); + CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); + //CheckParameter(StatFileFormat,); + CheckParameter(OrthoBoxTolerance, isPositive()); + CheckParameter(ThermIntDistSpringConst, isPositive()); + CheckParameter(ThermIntThetaSpringConst, isPositive()); + CheckParameter(ThermIntOmegaSpringConst, isPositive()); + CheckParameter(DampingAlpha,isNonNegative()); + CheckParameter(SkinThickness, isPositive()); + CheckParameter(Viscosity, isNonNegative()); + CheckParameter(BeadSize, isPositive()); + CheckParameter(FrozenBufferRadius, isPositive()); + CheckParameter(LangevinBufferRadius, isPositive()); + CheckParameter(NeighborListNeighbors, isPositive()); + + for(std::vector::iterator i = components_.begin(); i != components_.end(); ++i) { + if (!(*i)->findMoleculeStamp(moleculeStamps_)) { + std::ostringstream oss; + oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; + throw OOPSEException(oss.str()); + } + } +} + +bool Globals::addComponent(Component* comp) { + components_.push_back(comp); + return true; +} + +bool Globals::addZConsStamp(ZConsStamp* zcons) { + zconstraints_.push_back(zcons); + return true; +} + +bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { + std::string molStampName = molStamp->getName(); + std::map::iterator i; + bool ret = false; + i = moleculeStamps_.find(molStampName); + if (i == moleculeStamps_.end()) { + moleculeStamps_.insert(std::map::value_type(molStampName, molStamp)); + ret = true; + } else { + std::ostringstream oss; + oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; + throw OOPSEException(oss.str()); + } + return ret; +} + + +}