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#ifndef __GLOBALS_H__ |
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#define __GLOBALS_H__ |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#ifndef IO_GLOBALS_HPP |
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#define IO_GLOBALS_HPP |
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#include <iostream> |
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#include <stdlib.h> |
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#include <vector> |
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#include <string> |
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#include <map> |
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#include "BASS_interface.h" |
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#include "Component.hpp" |
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#include "LinkedCommand.hpp" |
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#include "MakeStamps.hpp" |
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#include "ZconStamp.hpp" |
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#include "types/Component.hpp" |
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#include "types/ZconsStamp.hpp" |
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#include "types/MoleculeStamp.hpp" |
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#include "utils/ParameterManager.hpp" |
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using namespace std; |
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namespace oopse { |
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class Globals : public DataHolder { |
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public: |
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typedef std::pair<int, int> intPair; |
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class Globals{ |
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|
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public: |
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|
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Globals(); |
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~Globals(); |
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|
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void initalize(); |
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|
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int newComponent( event* the_event ); |
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int componentAssign( event* the_event ); |
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int componentEnd( event* the_event ); |
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|
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int newZconstraint( event* the_event ); |
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int zConstraintAssign( event* the_event ); |
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int zConstraintEnd( event* the_event ); |
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|
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int globalAssign( event* the_event ); |
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int globalEnd( event* the_event ); |
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|
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char* getForceField( void ) { return force_field; } |
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int getNComponents( void ) { return n_components; } |
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double getTargetTemp( void ) { return target_temp; } |
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double getTargetPressure( void ) { return target_pressure; } |
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double getQmass( void ) { return q_mass; } |
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double getTauThermostat( void ) { return tau_thermostat; } |
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double getTauBarostat( void ) { return tau_barostat; } |
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char* getEnsemble( void ) { return ensemble; } |
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double getDt( void ) { return dt; } |
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double getRunTime( void ) { return run_time; } |
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|
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int getNzConstraints( void ) { return n_zConstraints; } |
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char* getInitialConfig( void ) { return initial_config; } |
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char* getFinalConfig( void ) { return final_config; } |
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int getNMol( void ) { return n_mol; } |
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double getDensity( void ) { return density; } |
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double getBox( void ) { return box; } |
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double getBoxX( void ) { return box_x; } |
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double getBoxY( void ) { return box_y; } |
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double getBoxZ( void ) { return box_z; } |
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double getSampleTime( void ) { return sample_time; } |
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double getStatusTime( void ) { return status_time; } |
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double getResetTime( void ) { return resetTime; } |
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double getThermalTime( void ) { return thermal_time; } |
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double getDielectric( void ) { return dielectric; } |
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double getRcut( void ) { return rcut; } |
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double getRsw( void ) { return rsw; } |
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int getTempSet( void ) { return tempSet; } |
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int getUseInitTime( void ) { return useInitTime; } |
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int getUseInitXSstate( void ) { return useInitXSstate; } |
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double getOrthoBoxTolerance(void) { return orthoBoxTolerance; } |
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int getPBC( void ) { return usePBC; } |
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int getUseRF( void ) { return useRF; } |
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char* getMixingRule( void) { return mixingRule; } |
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double getZconsTime(void) { return zcons_time; } |
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double getZconsTol(void) { return zcons_tol; } |
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char* getZconsForcePolicy(void) { return zconsForcePolicy; } |
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double getZconsGap(void) { return zcons_gap; } |
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double getZconsFixtime(void) { return zcons_fixtime; } |
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int getZconsUsingSMD(void) { return zcons_using_smd; } |
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int getSeed(void) { return seed; } |
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char* getMinimizer(void) { return minimizer_name; } |
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int getMinMaxIter(void) { return minimizer_maxiteration; } |
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int getMinWriteFrq(void) { return minimizer_writefrq; } |
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double getMinStepSize(void) { return minimizer_stepsize; } |
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double getMinFTol(void) { return minimizer_ftol; } |
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double getMinGTol(void) { return minimizer_gtol; } |
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double getMinLSTol(void) { return minimizer_ls_tol; } |
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int getMinLSMaxIter(void) { return minimizer_ls_maxiteration; } |
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int getUseSolidThermInt(void) { return useSolidThermInt; } |
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int getUseLiquidThermInt(void) { return useLiquidThermInt; } |
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double getThermIntLambda(void) { return thermodynamic_integration_lambda; } |
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double getThermIntK(void) { return thermodynamic_integration_k; } |
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char* getForceFieldVariant( void ) { return forcefield_variant; } |
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|
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short int haveDt( void ) { return have_dt; } |
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short int haveRunTime( void ) { return have_run_time; } |
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short int haveEnsemble( void ) { return have_ensemble; } |
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short int haveTargetTemp( void ) { return have_target_temp; } |
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short int haveInitialConfig( void ) { return have_initial_config; } |
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short int haveFinalConfig( void ) { return have_final_config; } |
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short int haveNMol( void ) { return have_n_mol; } |
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short int haveDensity( void ) { return have_density; } |
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short int haveBox( void ) { return have_box; } |
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short int haveBoxX( void ) { return have_box_x; } |
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short int haveBoxY( void ) { return have_box_y; } |
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short int haveBoxZ( void ) { return have_box_z; } |
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short int haveSampleTime( void ) { return have_sample_time; } |
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short int haveResetTime( void ) { return have_reset_time; } |
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short int haveStatusTime( void ) { return have_status_time; } |
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short int haveThermalTime( void ) { return have_thermal_time; } |
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short int haveRcut( void ) { return have_rcut; } |
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short int haveRsw( void ) { return have_rsw; } |
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short int haveDielectric( void ) { return have_dielectric; } |
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short int haveTempSet( void ) { return have_tempSet; } |
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short int haveTargetPressure( void ){ return have_target_pressure; } |
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short int haveQmass( void ) { return have_q_mass; } |
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short int haveTauThermostat( void ) { return have_tau_thermostat; } |
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short int haveTauBarostat( void ) { return have_tau_barostat; } |
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short int haveZconstraintTime(void) { return have_zcons_time; } |
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short int haveZconstraints( void ) { return have_zConstraints; } |
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short int haveZconsTol(void) { return have_zcons_tol; } |
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short int haveZconsForcePolicy(void){ return have_zcons_force_policy; } |
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short int haveZConsGap(void) { return have_zcons_gap; } |
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short int haveZConsFixTime(void) { return have_zcons_fixtime; } |
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short int haveZConsUsingSMD(void) { return have_zcons_using_smd; } |
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short int haveSeed(void) { return have_seed; } |
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short int haveMinimizer(void) { return have_minimizer; } |
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short int haveMinMaxIter(void) { return have_minimizer_maxiteration; } |
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short int haveMinWriteFrq(void) { return have_minimizer_writefrq; } |
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short int haveMinStepSize(void) { return have_minimizer_stepsize; } |
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short int haveMinFTol(void) { return have_minimizer_ftol; } |
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short int haveMinGTol(void) { return have_minimizer_gtol; } |
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short int haveMinLSTol(void) { return have_minimizer_ls_tol; } |
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short int haveMinLSMaxIter(void) { return have_minimizer_ls_maxiteration;} |
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short int haveThermIntLambda(void) { return have_thermodynamic_integration_lambda; } |
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short int haveThermIntK(void) { return have_thermodynamic_integration_k; } |
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short int haveForceFieldVariant(void) { return have_forcefield_variant; } |
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/* other accessors */ |
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Component** getComponents( void ) { return components; } |
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ZconStamp** getZconStamp( void ) { return zConstraints; } |
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private: |
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|
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int hash_size; |
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int hash_shift; |
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int hash( char* text ); |
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void addHash( char* text, int token ); |
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LinkedCommand** command_table; |
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char* checkMe( void ); |
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Component* current_component; |
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Component** components; // the array of components |
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ZconStamp* current_zConstraint; |
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ZconStamp** zConstraints; // the array of zConstraints |
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char force_field[100]; |
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int n_components; |
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int n_zConstraints; |
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double target_temp; |
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double target_pressure; |
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char ensemble[100]; |
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char mixingRule[100]; |
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double dt; |
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double run_time; |
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char initial_config[120]; |
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char final_config[120]; |
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int n_mol; |
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double density; |
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double box; |
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double box_x, box_y, box_z; |
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double sample_time; |
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double status_time; |
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double resetTime; |
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double orthoBoxTolerance; |
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double thermal_time; |
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double rcut; |
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double rsw; |
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double dielectric; |
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int tempSet; |
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int useInitTime; |
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int useInitXSstate; |
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int usePBC; |
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int useRF; |
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double q_mass; |
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double tau_thermostat; |
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double tau_barostat; |
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double zcons_time; |
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double zcons_tol; |
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char zconsForcePolicy[100]; |
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double zcons_gap; |
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double zcons_fixtime; |
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int zcons_using_smd; |
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|
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int seed; |
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char minimizer_name[100]; |
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int minimizer_maxiteration; |
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int minimizer_writefrq; |
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double minimizer_stepsize; |
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double minimizer_ftol; |
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double minimizer_gtol; |
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double minimizer_ls_tol; |
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int minimizer_ls_maxiteration; |
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int useSolidThermInt; |
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int useLiquidThermInt; |
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double thermodynamic_integration_lambda; |
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double thermodynamic_integration_k; |
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char forcefield_variant[100]; |
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|
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//required arguments |
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short int have_force_field, have_n_components, have_target_temp; |
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short int have_target_pressure, have_ensemble, have_dt, have_run_time; |
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|
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// optional arguments |
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short int have_initial_config, have_final_config, have_n_mol; |
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short int have_density, have_box, have_box_x, have_box_y, have_box_z; |
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short int have_sample_time, have_status_time, have_rcut, have_dielectric; |
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short int have_tempSet, have_thermal_time, have_rsw, have_q_mass; |
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short int have_tau_thermostat, have_tau_barostat; |
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short int have_zcons_time, have_zConstraints, have_n_zConstraints; |
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short int have_zcons_tol, have_seed; |
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short int have_zcons_force_policy, have_reset_time; |
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short int have_zcons_gap, have_zcons_fixtime; |
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short int have_zcons_using_smd; |
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short int have_minimizer, have_minimizer_maxiteration; |
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short int have_minimizer_writefrq, have_minimizer_stepsize; |
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short int have_minimizer_ftol, have_minimizer_gtol; |
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short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration; |
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short int have_thermodynamic_integration_lambda; |
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short int have_thermodynamic_integration_k; |
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short int have_forcefield_variant; |
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Globals(); |
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virtual ~Globals(); |
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|
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DeclareParameter(ForceField, std::string); |
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DeclareParameter(TargetTemp, RealType); |
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DeclareParameter(Ensemble, std::string); |
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DeclareParameter(Dt, RealType); |
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DeclareParameter(RunTime, RealType); |
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DeclareParameter(FinalConfig, std::string); |
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DeclareParameter(SampleTime, RealType); |
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DeclareParameter(ResetTime, RealType); |
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DeclareParameter(StatusTime, RealType); |
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DeclareParameter(CutoffRadius, RealType); |
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DeclareParameter(SwitchingRadius, RealType); |
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DeclareParameter(TempSet, bool); |
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DeclareParameter(ThermalTime, RealType); |
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DeclareParameter(UsePeriodicBoundaryConditions, bool); |
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DeclareParameter(TargetPressure, RealType); |
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DeclareParameter(UseAtomicVirial, bool); |
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DeclareParameter(TauThermostat, RealType); |
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DeclareParameter(TauBarostat, RealType); |
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DeclareParameter(ZconsTime, RealType); |
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DeclareParameter(ZconsTol, RealType); |
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DeclareParameter(ZconsForcePolicy, std::string); |
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DeclareParameter(Seed, unsigned long int); |
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DeclareParameter(UseInitalTime, bool); |
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DeclareParameter(UseIntialExtendedSystemState, bool); |
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DeclareParameter(OrthoBoxTolerance, RealType); |
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DeclareParameter(Minimizer, std::string); |
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DeclareParameter(MinimizerMaxIter, RealType); |
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DeclareParameter(MinimizerWriteFrq, int); |
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DeclareParameter(MinimizerStepSize, RealType); |
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DeclareParameter(MinimizerFTol, RealType); |
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DeclareParameter(MinimizerGTol, RealType); |
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DeclareParameter(MinimizerLSTol, RealType); |
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DeclareParameter(MinimizerLSMaxIter, int); |
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DeclareParameter(ZconsGap, RealType); |
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DeclareParameter(ZconsFixtime, RealType); |
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DeclareParameter(ZconsUsingSMD, bool); |
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DeclareParameter(UseSolidThermInt, bool); |
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DeclareParameter(UseLiquidThermInt, bool); |
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DeclareParameter(ThermodynamicIntegrationLambda, RealType); |
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DeclareParameter(ThermodynamicIntegrationK, RealType); |
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DeclareParameter(ForceFieldVariant, std::string); |
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DeclareParameter(ForceFieldFileName, std::string); |
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DeclareParameter(ThermIntDistSpringConst, RealType); |
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DeclareParameter(ThermIntThetaSpringConst, RealType); |
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DeclareParameter(ThermIntOmegaSpringConst, RealType); |
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DeclareParameter(SurfaceTension, RealType); |
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DeclareParameter(PrintPressureTensor, bool); |
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> |
DeclareParameter(TaggedAtomPair, intPair); |
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> |
DeclareParameter(PrintTaggedPairDistance, bool); |
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DeclareParameter(ElectrostaticSummationMethod, std::string); |
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> |
DeclareParameter(ElectrostaticScreeningMethod, std::string); |
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DeclareParameter(DampingAlpha, RealType); |
| 117 |
> |
DeclareParameter(Dielectric, RealType); |
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DeclareParameter(CutoffPolicy, std::string); |
| 119 |
> |
DeclareParameter(SwitchingFunctionType, std::string); |
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> |
DeclareParameter(CompressDumpFile, bool); |
| 121 |
> |
DeclareParameter(OutputForceVector, bool); |
| 122 |
> |
DeclareParameter(SkinThickness, RealType); |
| 123 |
> |
DeclareParameter(StatFileFormat, std::string); |
| 124 |
> |
DeclareParameter(HydroPropFile, std::string); |
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> |
DeclareParameter(Viscosity, RealType); |
| 126 |
> |
DeclareParameter(BeadSize, RealType); |
| 127 |
> |
DeclareParameter(ThermalConductivity, RealType); |
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> |
DeclareParameter(ThermalLength, RealType); |
| 129 |
> |
DeclareParameter(UseSphericalBoundaryConditions, bool); |
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> |
DeclareParameter(FrozenBufferRadius, RealType); |
| 131 |
> |
DeclareParameter(LangevinBufferRadius, RealType); |
| 132 |
> |
DeclareParameter(AccumulateBoxDipole, bool); |
| 133 |
> |
DeclareParameter(NeighborListNeighbors, int); |
| 134 |
> |
DeclareParameter(UseMultipleTemperatureMethod, bool); |
| 135 |
> |
DeclareParameter(MTM_Ce, RealType); |
| 136 |
> |
DeclareParameter(MTM_G, RealType); |
| 137 |
> |
DeclareParameter(MTM_Io, RealType); |
| 138 |
> |
DeclareParameter(MTM_Sigma, RealType); |
| 139 |
> |
DeclareParameter(MTM_R, RealType); |
| 140 |
> |
DeclareParameter(UseRNEMD, bool); |
| 141 |
> |
DeclareParameter(RNEMD_swapTime, RealType); |
| 142 |
> |
DeclareParameter(RNEMD_nBins, int); |
| 143 |
> |
DeclareParameter(RNEMD_swapType, std::string); |
| 144 |
> |
DeclareParameter(RNEMD_objectSelection, std::string); |
| 145 |
> |
DeclareParameter(UseRestraints, bool); |
| 146 |
> |
DeclareParameter(Restraint_objectSelection, std::string); |
| 147 |
> |
DeclareParameter(Restraint_type, std::string); |
| 148 |
> |
DeclareParameter(Restraint_file, std::string); |
| 149 |
> |
DeclareParameter(Restraint_DisplacementSpringConstant, RealType); |
| 150 |
> |
DeclareParameter(Restraint_RollSpringConstant, RealType); // phi |
| 151 |
> |
DeclareParameter(Restraint_PitchSpringConstant, RealType); // theta |
| 152 |
> |
DeclareParameter(Restraint_YawSpringConstant, RealType); // psi |
| 153 |
> |
|
| 154 |
> |
public: |
| 155 |
> |
bool addComponent(Component* comp); |
| 156 |
> |
bool addZConsStamp(ZConsStamp* zcons); |
| 157 |
> |
bool addMoleculeStamp(MoleculeStamp* molStamp); |
| 158 |
> |
int getNComponents() {return components_.size();} |
| 159 |
> |
std::vector<Component*> getComponents() {return components_;} |
| 160 |
> |
Component* getComponentAt(int index) {return components_.at(index);} |
| 161 |
> |
|
| 162 |
> |
int getNZconsStamps() {return zconstraints_.size();} |
| 163 |
> |
std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;} |
| 164 |
> |
ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);} |
| 165 |
> |
|
| 166 |
> |
virtual void validate(); |
| 167 |
> |
private: |
| 168 |
> |
|
| 169 |
> |
std::vector<Component*> components_; |
| 170 |
> |
std::vector<ZConsStamp*> zconstraints_; |
| 171 |
> |
std::map<std::string, MoleculeStamp*> moleculeStamps_; |
| 172 |
> |
std::pair<int, int> taggedAtomPair_; |
| 173 |
|
}; |
| 174 |
< |
|
| 174 |
> |
} |
| 175 |
|
#endif |
| 176 |
+ |
|
