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#include <algorithm> |
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#include <cstdlib> |
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#include <iostream> |
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#include <cmath> |
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#include <string> |
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|
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#include "Integrator.hpp" |
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#include "simError.h" |
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#include "mpiSimulation.hpp" |
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#endif |
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|
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// some defines for ensemble and Forcefield cases |
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|
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#define NVE_ENS 0 |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTim_ENS 4 |
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#define NPTfm_ENS 5 |
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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|
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using namespace std; |
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|
33 |
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SimSetup::SimSetup(){ |
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|
35 |
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isInfoArray = 0; |
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nInfo = 1; |
37 |
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|
38 |
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stamps = new MakeStamps(); |
39 |
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globals = new Globals(); |
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|
41 |
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|
42 |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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MPIcheckPoint(); |
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delete globals; |
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} |
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|
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void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
54 |
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info = the_info; |
55 |
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nInfo = theNinfo; |
56 |
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isInfoArray = 1; |
57 |
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} |
58 |
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|
59 |
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|
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void SimSetup::parseFile( char* fileName ){ |
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|
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#ifdef IS_MPI |
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|
93 |
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#endif // is_mpi |
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|
95 |
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void SimSetup::createSim( void ){ |
95 |
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void SimSetup::createSim(void){ |
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|
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MakeStamps *the_stamps; |
68 |
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Globals* the_globals; |
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int i, j; |
70 |
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|
71 |
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// get the stamps and globals; |
72 |
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the_stamps = stamps; |
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the_globals = globals; |
74 |
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|
75 |
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// set the easy ones first |
76 |
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simnfo->target_temp = the_globals->getTargetTemp(); |
77 |
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simnfo->dt = the_globals->getDt(); |
78 |
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simnfo->run_time = the_globals->getRunTime(); |
79 |
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|
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// get the ones we know are there, yet still may need some work. |
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n_components = the_globals->getNComponents(); |
82 |
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strcpy( force_field, the_globals->getForceField() ); |
83 |
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strcpy( ensemble, the_globals->getEnsemble() ); |
84 |
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strcpy( simnfo->ensemble, ensemble ); |
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|
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strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 |
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simnfo->usePBC = the_globals->getPBC(); |
88 |
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|
89 |
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|
90 |
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|
91 |
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if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 |
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else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
93 |
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else{ |
94 |
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sprintf( painCave.errMsg, |
95 |
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"SimSetup Error. Unrecognized force field -> %s\n", |
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force_field ); |
97 |
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painCave.isFatal = 1; |
98 |
< |
simError(); |
99 |
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} |
100 |
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|
101 |
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "ForceField creation successful" ); |
103 |
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MPIcheckPoint(); |
104 |
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#endif // is_mpi |
105 |
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|
97 |
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int i, j, k, globalAtomIndex; |
98 |
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|
99 |
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// gather all of the information from the Bass file |
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|
101 |
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// get the components and calculate the tot_nMol and indvidual n_mol |
109 |
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the_components = the_globals->getComponents(); |
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components_nmol = new int[n_components]; |
111 |
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comp_stamps = new MoleculeStamp*[n_components]; |
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gatherInfo(); |
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|
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if( !the_globals->haveNMol() ){ |
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// we don't have the total number of molecules, so we assume it is |
115 |
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// given in each component |
103 |
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// creation of complex system objects |
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|
105 |
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tot_nmol = 0; |
118 |
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for( i=0; i<n_components; i++ ){ |
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sysObjectsCreation(); |
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|
107 |
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if( !the_components[i]->haveNMol() ){ |
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// we have a problem |
122 |
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sprintf( painCave.errMsg, |
123 |
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"SimSetup Error. No global NMol or component NMol" |
124 |
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" given. Cannot calculate the number of atoms.\n" ); |
125 |
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painCave.isFatal = 1; |
126 |
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simError(); |
127 |
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} |
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// check on the post processing info |
108 |
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|
109 |
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tot_nmol += the_components[i]->getNMol(); |
130 |
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components_nmol[i] = the_components[i]->getNMol(); |
131 |
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} |
132 |
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} |
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else{ |
134 |
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sprintf( painCave.errMsg, |
135 |
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"SimSetup error.\n" |
136 |
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"\tSorry, the ability to specify total" |
137 |
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" nMols and then give molfractions in the components\n" |
138 |
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"\tis not currently supported." |
139 |
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" Please give nMol in the components.\n" ); |
140 |
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painCave.isFatal = 1; |
141 |
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simError(); |
142 |
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|
143 |
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|
144 |
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// tot_nmol = the_globals->getNMol(); |
145 |
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|
146 |
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// //we have the total number of molecules, now we check for molfractions |
147 |
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// for( i=0; i<n_components; i++ ){ |
148 |
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|
149 |
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// if( !the_components[i]->haveMolFraction() ){ |
150 |
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|
151 |
< |
// if( !the_components[i]->haveNMol() ){ |
152 |
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// //we have a problem |
153 |
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// std::cerr << "SimSetup error. Neither molFraction nor " |
154 |
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// << " nMol was given in component |
155 |
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|
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} |
109 |
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finalInfoCheck(); |
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "Have the number of components" ); |
160 |
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MPIcheckPoint(); |
161 |
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#endif // is_mpi |
111 |
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// initialize the system coordinates |
112 |
|
|
113 |
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// make an array of molecule stamps that match the components used. |
164 |
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// also extract the used stamps out into a separate linked list |
113 |
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if( !isInfoArray ) initSystemCoords(); |
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|
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simnfo->nComponents = n_components; |
167 |
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simnfo->componentsNmol = components_nmol; |
168 |
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simnfo->compStamps = comp_stamps; |
169 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
170 |
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|
171 |
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char* id; |
172 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
173 |
< |
LinkedMolStamp* currentStamp = NULL; |
174 |
< |
for( i=0; i<n_components; i++ ){ |
175 |
< |
|
176 |
< |
id = the_components[i]->getType(); |
177 |
< |
comp_stamps[i] = NULL; |
178 |
< |
|
179 |
< |
// check to make sure the component isn't already in the list |
180 |
< |
|
181 |
< |
comp_stamps[i] = headStamp->match( id ); |
182 |
< |
if( comp_stamps[i] == NULL ){ |
183 |
< |
|
184 |
< |
// extract the component from the list; |
185 |
< |
|
186 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
187 |
< |
if( currentStamp == NULL ){ |
188 |
< |
sprintf( painCave.errMsg, |
189 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
190 |
< |
"list of declared molecules\n", |
191 |
< |
id ); |
192 |
< |
painCave.isFatal = 1; |
193 |
< |
simError(); |
194 |
< |
} |
195 |
< |
|
196 |
< |
headStamp->add( currentStamp ); |
197 |
< |
comp_stamps[i] = headStamp->match( id ); |
198 |
< |
} |
199 |
< |
} |
200 |
< |
|
201 |
< |
#ifdef IS_MPI |
202 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
203 |
< |
MPIcheckPoint(); |
204 |
< |
#endif // is_mpi |
205 |
< |
|
206 |
< |
|
207 |
< |
|
208 |
< |
|
209 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
210 |
< |
|
211 |
< |
tot_atoms = 0; |
212 |
< |
tot_bonds = 0; |
213 |
< |
tot_bends = 0; |
214 |
< |
tot_torsions = 0; |
215 |
< |
for( i=0; i<n_components; i++ ){ |
216 |
< |
|
217 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
220 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
221 |
< |
} |
222 |
< |
|
223 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
224 |
< |
|
225 |
< |
simnfo->n_atoms = tot_atoms; |
226 |
< |
simnfo->n_bonds = tot_bonds; |
227 |
< |
simnfo->n_bends = tot_bends; |
228 |
< |
simnfo->n_torsions = tot_torsions; |
229 |
< |
simnfo->n_SRI = tot_SRI; |
230 |
< |
simnfo->n_mol = tot_nmol; |
231 |
< |
|
232 |
< |
|
233 |
< |
#ifdef IS_MPI |
234 |
< |
|
235 |
< |
// divide the molecules among processors here. |
236 |
< |
|
237 |
< |
mpiSim = new mpiSimulation( simnfo ); |
238 |
< |
|
239 |
< |
|
240 |
< |
|
241 |
< |
globalIndex = mpiSim->divideLabor(); |
242 |
< |
|
243 |
< |
// set up the local variables |
244 |
< |
|
245 |
< |
int localMol, allMol; |
246 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
247 |
< |
|
248 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
249 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
250 |
< |
|
251 |
< |
allMol = 0; |
252 |
< |
localMol = 0; |
253 |
< |
local_atoms = 0; |
254 |
< |
local_bonds = 0; |
255 |
< |
local_bends = 0; |
256 |
< |
local_torsions = 0; |
257 |
< |
for( i=0; i<n_components; i++ ){ |
258 |
< |
|
259 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
260 |
< |
|
261 |
< |
if( mol2proc[j] == worldRank ){ |
262 |
< |
|
263 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
264 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
265 |
< |
local_bends += comp_stamps[i]->getNBends(); |
266 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
267 |
< |
localMol++; |
268 |
< |
} |
269 |
< |
allMol++; |
270 |
< |
} |
271 |
< |
} |
272 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
273 |
< |
|
274 |
< |
|
275 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
276 |
< |
|
277 |
< |
if( local_atoms != simnfo->n_atoms ){ |
278 |
< |
sprintf( painCave.errMsg, |
279 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
280 |
< |
" localAtom (%d) are not equal.\n", |
281 |
< |
simnfo->n_atoms, |
282 |
< |
local_atoms ); |
283 |
< |
painCave.isFatal = 1; |
284 |
< |
simError(); |
285 |
< |
} |
286 |
< |
|
287 |
< |
simnfo->n_bonds = local_bonds; |
288 |
< |
simnfo->n_bends = local_bends; |
289 |
< |
simnfo->n_torsions = local_torsions; |
290 |
< |
simnfo->n_SRI = local_SRI; |
291 |
< |
simnfo->n_mol = localMol; |
292 |
< |
|
293 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
294 |
< |
MPIcheckPoint(); |
295 |
< |
|
296 |
< |
|
297 |
< |
#endif // is_mpi |
298 |
< |
|
299 |
< |
|
300 |
< |
// create the atom and short range interaction arrays |
301 |
< |
|
302 |
< |
Atom::createArrays(simnfo->n_atoms); |
303 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
304 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
305 |
< |
int molIndex; |
115 |
> |
// make the output filenames |
116 |
|
|
117 |
< |
// initialize the molecule's stampID's |
308 |
< |
|
309 |
< |
#ifdef IS_MPI |
310 |
< |
|
311 |
< |
|
312 |
< |
molIndex = 0; |
313 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
314 |
< |
|
315 |
< |
if(mol2proc[i] == worldRank ){ |
316 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
317 |
< |
molIndex++; |
318 |
< |
} |
319 |
< |
} |
320 |
< |
|
321 |
< |
#else // is_mpi |
322 |
< |
|
323 |
< |
molIndex = 0; |
324 |
< |
for(i=0; i<n_components; i++){ |
325 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
326 |
< |
the_molecules[molIndex].setStampID( i ); |
327 |
< |
molIndex++; |
328 |
< |
} |
329 |
< |
} |
330 |
< |
|
331 |
< |
|
332 |
< |
#endif // is_mpi |
333 |
< |
|
334 |
< |
|
335 |
< |
if( simnfo->n_SRI ){ |
336 |
< |
|
337 |
< |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 |
< |
|
339 |
< |
Exclude::createArray(simnfo->n_SRI); |
340 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
341 |
< |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
342 |
< |
simnfo->globalExcludes = new int; |
343 |
< |
simnfo->n_exclude = tot_SRI; |
344 |
< |
} |
345 |
< |
else{ |
346 |
< |
|
347 |
< |
Exclude::createArray( 1 ); |
348 |
< |
the_excludes = new Exclude*; |
349 |
< |
the_excludes[0] = new Exclude(0); |
350 |
< |
the_excludes[0]->setPair( 0,0 ); |
351 |
< |
simnfo->globalExcludes = new int; |
352 |
< |
simnfo->globalExcludes[0] = 0; |
353 |
< |
simnfo->n_exclude = 0; |
354 |
< |
} |
355 |
< |
|
356 |
< |
// set the arrays into the SimInfo object |
357 |
< |
|
358 |
< |
simnfo->atoms = the_atoms; |
359 |
< |
simnfo->molecules = the_molecules; |
360 |
< |
simnfo->nGlobalExcludes = 0; |
361 |
< |
simnfo->excludes = the_excludes; |
362 |
< |
|
363 |
< |
|
364 |
< |
// get some of the tricky things that may still be in the globals |
365 |
< |
|
366 |
< |
|
367 |
< |
if( the_globals->haveBox() ){ |
368 |
< |
simnfo->box_x = the_globals->getBox(); |
369 |
< |
simnfo->box_y = the_globals->getBox(); |
370 |
< |
simnfo->box_z = the_globals->getBox(); |
371 |
< |
} |
372 |
< |
else if( the_globals->haveDensity() ){ |
373 |
< |
|
374 |
< |
double vol; |
375 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
376 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
377 |
< |
simnfo->box_y = simnfo->box_x; |
378 |
< |
simnfo->box_z = simnfo->box_x; |
379 |
< |
} |
380 |
< |
else{ |
381 |
< |
if( !the_globals->haveBoxX() ){ |
382 |
< |
sprintf( painCave.errMsg, |
383 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
384 |
< |
painCave.isFatal = 1; |
385 |
< |
simError(); |
386 |
< |
} |
387 |
< |
simnfo->box_x = the_globals->getBoxX(); |
388 |
< |
|
389 |
< |
if( !the_globals->haveBoxY() ){ |
390 |
< |
sprintf( painCave.errMsg, |
391 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
392 |
< |
painCave.isFatal = 1; |
393 |
< |
simError(); |
394 |
< |
} |
395 |
< |
simnfo->box_y = the_globals->getBoxY(); |
396 |
< |
|
397 |
< |
if( !the_globals->haveBoxZ() ){ |
398 |
< |
sprintf( painCave.errMsg, |
399 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
400 |
< |
painCave.isFatal = 1; |
401 |
< |
simError(); |
402 |
< |
} |
403 |
< |
simnfo->box_z = the_globals->getBoxZ(); |
404 |
< |
} |
405 |
< |
|
406 |
< |
#ifdef IS_MPI |
407 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
408 |
< |
MPIcheckPoint(); |
409 |
< |
#endif // is_mpi |
410 |
< |
|
411 |
< |
|
412 |
< |
// initialize the arrays |
413 |
< |
|
414 |
< |
the_ff->setSimInfo( simnfo ); |
415 |
< |
|
416 |
< |
makeMolecules(); |
417 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
418 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
419 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
420 |
< |
} |
421 |
< |
|
422 |
< |
if (the_globals->getUseRF() ) { |
423 |
< |
simnfo->useReactionField = 1; |
424 |
< |
|
425 |
< |
if( !the_globals->haveECR() ){ |
426 |
< |
sprintf( painCave.errMsg, |
427 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
428 |
< |
"box length for the electrostaticCutoffRadius.\n" |
429 |
< |
"I hope you have a very fast processor!\n"); |
430 |
< |
painCave.isFatal = 0; |
431 |
< |
simError(); |
432 |
< |
double smallest; |
433 |
< |
smallest = simnfo->box_x; |
434 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
435 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
436 |
< |
simnfo->ecr = 0.5 * smallest; |
437 |
< |
} else { |
438 |
< |
simnfo->ecr = the_globals->getECR(); |
439 |
< |
} |
440 |
< |
|
441 |
< |
if( !the_globals->haveEST() ){ |
442 |
< |
sprintf( painCave.errMsg, |
443 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
444 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
445 |
< |
); |
446 |
< |
painCave.isFatal = 0; |
447 |
< |
simError(); |
448 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
449 |
< |
} else { |
450 |
< |
simnfo->est = the_globals->getEST(); |
451 |
< |
} |
452 |
< |
|
453 |
< |
if(!the_globals->haveDielectric() ){ |
454 |
< |
sprintf( painCave.errMsg, |
455 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
456 |
< |
"setting a dielectric constant!\n" |
457 |
< |
); |
458 |
< |
painCave.isFatal = 1; |
459 |
< |
simError(); |
460 |
< |
} |
461 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
462 |
< |
} else { |
463 |
< |
if (simnfo->n_dipoles) { |
464 |
< |
|
465 |
< |
if( !the_globals->haveECR() ){ |
466 |
< |
sprintf( painCave.errMsg, |
467 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
468 |
< |
"box length for the electrostaticCutoffRadius.\n" |
469 |
< |
"I hope you have a very fast processor!\n"); |
470 |
< |
painCave.isFatal = 0; |
471 |
< |
simError(); |
472 |
< |
double smallest; |
473 |
< |
smallest = simnfo->box_x; |
474 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
475 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
476 |
< |
simnfo->ecr = 0.5 * smallest; |
477 |
< |
} else { |
478 |
< |
simnfo->ecr = the_globals->getECR(); |
479 |
< |
} |
480 |
< |
|
481 |
< |
if( !the_globals->haveEST() ){ |
482 |
< |
sprintf( painCave.errMsg, |
483 |
< |
"SimSetup Warning: using default value of 5% of the" |
484 |
< |
"electrostaticCutoffRadius for the " |
485 |
< |
"electrostaticSkinThickness\n" |
486 |
< |
); |
487 |
< |
painCave.isFatal = 0; |
488 |
< |
simError(); |
489 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
490 |
< |
} else { |
491 |
< |
simnfo->est = the_globals->getEST(); |
492 |
< |
} |
493 |
< |
} |
494 |
< |
} |
495 |
< |
|
496 |
< |
#ifdef IS_MPI |
497 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
498 |
< |
MPIcheckPoint(); |
499 |
< |
#endif // is_mpi |
500 |
< |
|
501 |
< |
if( the_globals->haveInitialConfig() ){ |
502 |
< |
|
503 |
< |
InitializeFromFile* fileInit; |
504 |
< |
#ifdef IS_MPI // is_mpi |
505 |
< |
if( worldRank == 0 ){ |
506 |
< |
#endif //is_mpi |
507 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
508 |
< |
#ifdef IS_MPI |
509 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
510 |
< |
#endif |
511 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
512 |
< |
|
513 |
< |
delete fileInit; |
514 |
< |
} |
515 |
< |
else{ |
516 |
< |
|
517 |
< |
#ifdef IS_MPI |
518 |
< |
|
519 |
< |
// no init from bass |
520 |
< |
|
521 |
< |
sprintf( painCave.errMsg, |
522 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
523 |
< |
painCave.isFatal; |
524 |
< |
simError(); |
525 |
< |
|
526 |
< |
#else |
527 |
< |
|
528 |
< |
initFromBass(); |
529 |
< |
|
530 |
< |
|
531 |
< |
#endif |
532 |
< |
} |
533 |
< |
|
534 |
< |
#ifdef IS_MPI |
535 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
536 |
< |
MPIcheckPoint(); |
537 |
< |
#endif // is_mpi |
538 |
< |
|
539 |
< |
|
117 |
> |
makeOutNames(); |
118 |
|
|
119 |
< |
|
119 |
> |
// make the integrator |
120 |
|
|
121 |
< |
|
544 |
< |
|
545 |
< |
#ifdef IS_MPI |
546 |
< |
if( worldRank == 0 ){ |
547 |
< |
#endif // is_mpi |
548 |
< |
|
549 |
< |
if( the_globals->haveFinalConfig() ){ |
550 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
551 |
< |
} |
552 |
< |
else{ |
553 |
< |
strcpy( simnfo->finalName, inFileName ); |
554 |
< |
char* endTest; |
555 |
< |
int nameLength = strlen( simnfo->finalName ); |
556 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
557 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
558 |
< |
strcpy( endTest, ".eor" ); |
559 |
< |
} |
560 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
561 |
< |
strcpy( endTest, ".eor" ); |
562 |
< |
} |
563 |
< |
else{ |
564 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
565 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
566 |
< |
strcpy( endTest, ".eor" ); |
567 |
< |
} |
568 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
569 |
< |
strcpy( endTest, ".eor" ); |
570 |
< |
} |
571 |
< |
else{ |
572 |
< |
strcat( simnfo->finalName, ".eor" ); |
573 |
< |
} |
574 |
< |
} |
575 |
< |
} |
576 |
< |
|
577 |
< |
// make the sample and status out names |
578 |
< |
|
579 |
< |
strcpy( simnfo->sampleName, inFileName ); |
580 |
< |
char* endTest; |
581 |
< |
int nameLength = strlen( simnfo->sampleName ); |
582 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
583 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
584 |
< |
strcpy( endTest, ".dump" ); |
585 |
< |
} |
586 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
587 |
< |
strcpy( endTest, ".dump" ); |
588 |
< |
} |
589 |
< |
else{ |
590 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
591 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
592 |
< |
strcpy( endTest, ".dump" ); |
593 |
< |
} |
594 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
595 |
< |
strcpy( endTest, ".dump" ); |
596 |
< |
} |
597 |
< |
else{ |
598 |
< |
strcat( simnfo->sampleName, ".dump" ); |
599 |
< |
} |
600 |
< |
} |
601 |
< |
|
602 |
< |
strcpy( simnfo->statusName, inFileName ); |
603 |
< |
nameLength = strlen( simnfo->statusName ); |
604 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
605 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
606 |
< |
strcpy( endTest, ".stat" ); |
607 |
< |
} |
608 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
609 |
< |
strcpy( endTest, ".stat" ); |
610 |
< |
} |
611 |
< |
else{ |
612 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
613 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
614 |
< |
strcpy( endTest, ".stat" ); |
615 |
< |
} |
616 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
617 |
< |
strcpy( endTest, ".stat" ); |
618 |
< |
} |
619 |
< |
else{ |
620 |
< |
strcat( simnfo->statusName, ".stat" ); |
621 |
< |
} |
622 |
< |
} |
623 |
< |
|
624 |
< |
#ifdef IS_MPI |
625 |
< |
} |
626 |
< |
#endif // is_mpi |
121 |
> |
makeIntegrator(); |
122 |
|
|
628 |
– |
// set the status, sample, and themal kick times |
629 |
– |
|
630 |
– |
if( the_globals->haveSampleTime() ){ |
631 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
632 |
– |
simnfo->statusTime = simnfo->sampleTime; |
633 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
634 |
– |
} |
635 |
– |
else{ |
636 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
637 |
– |
simnfo->statusTime = simnfo->sampleTime; |
638 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
639 |
– |
} |
640 |
– |
|
641 |
– |
if( the_globals->haveStatusTime() ){ |
642 |
– |
simnfo->statusTime = the_globals->getStatusTime(); |
643 |
– |
} |
644 |
– |
|
645 |
– |
if( the_globals->haveThermalTime() ){ |
646 |
– |
simnfo->thermalTime = the_globals->getThermalTime(); |
647 |
– |
} |
648 |
– |
|
649 |
– |
// check for the temperature set flag |
650 |
– |
|
651 |
– |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
652 |
– |
|
653 |
– |
|
654 |
– |
// // make the longe range forces and the integrator |
655 |
– |
|
656 |
– |
// new AllLong( simnfo ); |
657 |
– |
|
658 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
659 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
660 |
– |
|
123 |
|
#ifdef IS_MPI |
124 |
|
mpiSim->mpiRefresh(); |
125 |
|
#endif |
126 |
|
|
127 |
|
// initialize the Fortran |
128 |
|
|
129 |
+ |
initFortran(); |
130 |
|
|
668 |
– |
simnfo->refreshSim(); |
669 |
– |
|
670 |
– |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
671 |
– |
the_ff->initForceField( LB_MIXING_RULE ); |
672 |
– |
} |
673 |
– |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
674 |
– |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
675 |
– |
} |
676 |
– |
else{ |
677 |
– |
sprintf( painCave.errMsg, |
678 |
– |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
679 |
– |
simnfo->mixingRule ); |
680 |
– |
painCave.isFatal = 1; |
681 |
– |
simError(); |
682 |
– |
} |
131 |
|
|
132 |
|
|
685 |
– |
#ifdef IS_MPI |
686 |
– |
strcpy( checkPointMsg, |
687 |
– |
"Successfully intialized the mixingRule for Fortran." ); |
688 |
– |
MPIcheckPoint(); |
689 |
– |
#endif // is_mpi |
133 |
|
} |
134 |
|
|
135 |
|
|
136 |
|
void SimSetup::makeMolecules( void ){ |
137 |
|
|
138 |
+ |
int k,l; |
139 |
|
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
140 |
< |
molInit info; |
140 |
> |
molInit molInfo; |
141 |
|
DirectionalAtom* dAtom; |
142 |
|
LinkedAssign* extras; |
143 |
|
LinkedAssign* current_extra; |
160 |
|
|
161 |
|
double ux, uy, uz, u, uSqr; |
162 |
|
|
163 |
< |
atomOffset = 0; |
720 |
< |
excludeOffset = 0; |
721 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
163 |
> |
for(k=0; k<nInfo; k++){ |
164 |
|
|
165 |
< |
stampID = the_molecules[i].getStampID(); |
165 |
> |
the_ff->setSimInfo( &(info[k]) ); |
166 |
|
|
167 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
168 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
169 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
170 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
171 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
167 |
> |
atomOffset = 0; |
168 |
> |
excludeOffset = 0; |
169 |
> |
for(i=0; i<info[k].n_mol; i++){ |
170 |
> |
|
171 |
> |
stampID = info[k].molecules[i].getStampID(); |
172 |
|
|
173 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
174 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
175 |
< |
info.myBonds = new Bond*[info.nBonds]; |
176 |
< |
info.myBends = new Bend*[info.nBends]; |
177 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
173 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
174 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
175 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
176 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
177 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
178 |
> |
|
179 |
> |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
180 |
> |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
181 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
182 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
183 |
> |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
184 |
|
|
185 |
< |
theBonds = new bond_pair[info.nBonds]; |
186 |
< |
theBends = new bend_set[info.nBends]; |
187 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
185 |
> |
theBonds = new bond_pair[molInfo.nBonds]; |
186 |
> |
theBends = new bend_set[molInfo.nBends]; |
187 |
> |
theTorsions = new torsion_set[molInfo.nTorsions]; |
188 |
|
|
189 |
< |
// make the Atoms |
189 |
> |
// make the Atoms |
190 |
|
|
191 |
< |
for(j=0; j<info.nAtoms; j++){ |
744 |
< |
|
745 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
746 |
< |
if( currentAtom->haveOrientation() ){ |
191 |
> |
for(j=0; j<molInfo.nAtoms; j++){ |
192 |
|
|
193 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
194 |
< |
simnfo->n_oriented++; |
195 |
< |
info.myAtoms[j] = dAtom; |
196 |
< |
|
197 |
< |
ux = currentAtom->getOrntX(); |
198 |
< |
uy = currentAtom->getOrntY(); |
199 |
< |
uz = currentAtom->getOrntZ(); |
200 |
< |
|
201 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
202 |
< |
|
203 |
< |
u = sqrt( uSqr ); |
204 |
< |
ux = ux / u; |
205 |
< |
uy = uy / u; |
206 |
< |
uz = uz / u; |
207 |
< |
|
208 |
< |
dAtom->setSUx( ux ); |
209 |
< |
dAtom->setSUy( uy ); |
210 |
< |
dAtom->setSUz( uz ); |
211 |
< |
} |
212 |
< |
else{ |
213 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
214 |
< |
} |
215 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
193 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 |
> |
if( currentAtom->haveOrientation() ){ |
195 |
> |
|
196 |
> |
dAtom = new DirectionalAtom( (j + atomOffset), |
197 |
> |
info[k].getConfiguration() ); |
198 |
> |
info[k].n_oriented++; |
199 |
> |
molInfo.myAtoms[j] = dAtom; |
200 |
> |
|
201 |
> |
ux = currentAtom->getOrntX(); |
202 |
> |
uy = currentAtom->getOrntY(); |
203 |
> |
uz = currentAtom->getOrntZ(); |
204 |
> |
|
205 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 |
> |
|
207 |
> |
u = sqrt( uSqr ); |
208 |
> |
ux = ux / u; |
209 |
> |
uy = uy / u; |
210 |
> |
uz = uz / u; |
211 |
> |
|
212 |
> |
dAtom->setSUx( ux ); |
213 |
> |
dAtom->setSUy( uy ); |
214 |
> |
dAtom->setSUz( uz ); |
215 |
> |
} |
216 |
> |
else{ |
217 |
> |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 |
> |
info[k].getConfiguration() ); |
219 |
> |
} |
220 |
> |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 |
|
|
222 |
|
#ifdef IS_MPI |
223 |
|
|
224 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 |
|
|
226 |
|
#endif // is_mpi |
227 |
< |
} |
227 |
> |
} |
228 |
|
|
229 |
|
// make the bonds |
230 |
< |
for(j=0; j<info.nBonds; j++){ |
230 |
> |
for(j=0; j<molInfo.nBonds; j++){ |
231 |
|
|
232 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
233 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
234 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
235 |
< |
|
236 |
< |
exI = theBonds[i].a; |
237 |
< |
exJ = theBonds[i].b; |
238 |
< |
|
239 |
< |
// exclude_I must always be the smaller of the pair |
240 |
< |
if( exI > exJ ){ |
241 |
< |
tempEx = exI; |
242 |
< |
exI = exJ; |
243 |
< |
exJ = tempEx; |
244 |
< |
} |
232 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
233 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
234 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
235 |
> |
|
236 |
> |
exI = theBonds[j].a; |
237 |
> |
exJ = theBonds[j].b; |
238 |
> |
|
239 |
> |
// exclude_I must always be the smaller of the pair |
240 |
> |
if( exI > exJ ){ |
241 |
> |
tempEx = exI; |
242 |
> |
exI = exJ; |
243 |
> |
exJ = tempEx; |
244 |
> |
} |
245 |
|
#ifdef IS_MPI |
246 |
< |
tempEx = exI; |
247 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
248 |
< |
tempEx = exJ; |
249 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
250 |
< |
|
251 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
246 |
> |
tempEx = exI; |
247 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 |
> |
tempEx = exJ; |
249 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 |
> |
|
251 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
252 |
|
#else // isn't MPI |
253 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
253 |
> |
|
254 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
255 |
|
#endif //is_mpi |
256 |
< |
} |
257 |
< |
excludeOffset += info.nBonds; |
807 |
< |
|
808 |
< |
//make the bends |
809 |
< |
for(j=0; j<info.nBends; j++){ |
256 |
> |
} |
257 |
> |
excludeOffset += molInfo.nBonds; |
258 |
|
|
259 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
260 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
261 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
262 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
259 |
> |
//make the bends |
260 |
> |
for(j=0; j<molInfo.nBends; j++){ |
261 |
> |
|
262 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
263 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
264 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
265 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
266 |
> |
|
267 |
> |
if( currentBend->haveExtras() ){ |
268 |
|
|
269 |
< |
if( currentBend->haveExtras() ){ |
270 |
< |
|
271 |
< |
extras = currentBend->getExtras(); |
272 |
< |
current_extra = extras; |
273 |
< |
|
274 |
< |
while( current_extra != NULL ){ |
275 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
269 |
> |
extras = currentBend->getExtras(); |
270 |
> |
current_extra = extras; |
271 |
> |
|
272 |
> |
while( current_extra != NULL ){ |
273 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 |
> |
|
275 |
> |
switch( current_extra->getType() ){ |
276 |
|
|
277 |
< |
switch( current_extra->getType() ){ |
277 |
> |
case 0: |
278 |
> |
theBends[j].ghost = |
279 |
> |
current_extra->getInt() + atomOffset; |
280 |
> |
theBends[j].isGhost = 1; |
281 |
> |
break; |
282 |
> |
|
283 |
> |
case 1: |
284 |
> |
theBends[j].ghost = |
285 |
> |
(int)current_extra->getDouble() + atomOffset; |
286 |
> |
theBends[j].isGhost = 1; |
287 |
> |
break; |
288 |
> |
|
289 |
> |
default: |
290 |
> |
sprintf( painCave.errMsg, |
291 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
292 |
> |
"double nor an int.\n" |
293 |
> |
"-->Bend[%d] in %s\n", |
294 |
> |
j, comp_stamps[stampID]->getID() ); |
295 |
> |
painCave.isFatal = 1; |
296 |
> |
simError(); |
297 |
> |
} |
298 |
> |
} |
299 |
> |
|
300 |
> |
else{ |
301 |
|
|
826 |
– |
case 0: |
827 |
– |
theBends[j].ghost = |
828 |
– |
current_extra->getInt() + atomOffset; |
829 |
– |
theBends[j].isGhost = 1; |
830 |
– |
break; |
831 |
– |
|
832 |
– |
case 1: |
833 |
– |
theBends[j].ghost = |
834 |
– |
(int)current_extra->getDouble() + atomOffset; |
835 |
– |
theBends[j].isGhost = 1; |
836 |
– |
break; |
837 |
– |
|
838 |
– |
default: |
302 |
|
sprintf( painCave.errMsg, |
303 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
304 |
< |
"double nor an int.\n" |
305 |
< |
"-->Bend[%d] in %s\n", |
303 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
304 |
> |
" -->%s in Bend[%d] in %s\n", |
305 |
> |
current_extra->getlhs(), |
306 |
|
j, comp_stamps[stampID]->getID() ); |
307 |
|
painCave.isFatal = 1; |
308 |
|
simError(); |
309 |
|
} |
847 |
– |
} |
848 |
– |
|
849 |
– |
else{ |
310 |
|
|
311 |
< |
sprintf( painCave.errMsg, |
852 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
853 |
< |
" -->%s in Bend[%d] in %s\n", |
854 |
< |
current_extra->getlhs(), |
855 |
< |
j, comp_stamps[stampID]->getID() ); |
856 |
< |
painCave.isFatal = 1; |
857 |
< |
simError(); |
311 |
> |
current_extra = current_extra->getNext(); |
312 |
|
} |
313 |
+ |
} |
314 |
+ |
|
315 |
+ |
if( !theBends[j].isGhost ){ |
316 |
|
|
317 |
< |
current_extra = current_extra->getNext(); |
317 |
> |
exI = theBends[j].a; |
318 |
> |
exJ = theBends[j].c; |
319 |
|
} |
320 |
< |
} |
320 |
> |
else{ |
321 |
|
|
322 |
< |
if( !theBends[j].isGhost ){ |
323 |
< |
|
324 |
< |
exI = theBends[j].a; |
867 |
< |
exJ = theBends[j].c; |
868 |
< |
} |
869 |
< |
else{ |
322 |
> |
exI = theBends[j].a; |
323 |
> |
exJ = theBends[j].b; |
324 |
> |
} |
325 |
|
|
326 |
< |
exI = theBends[j].a; |
327 |
< |
exJ = theBends[j].b; |
328 |
< |
} |
329 |
< |
|
330 |
< |
// exclude_I must always be the smaller of the pair |
331 |
< |
if( exI > exJ ){ |
326 |
> |
// exclude_I must always be the smaller of the pair |
327 |
> |
if( exI > exJ ){ |
328 |
> |
tempEx = exI; |
329 |
> |
exI = exJ; |
330 |
> |
exJ = tempEx; |
331 |
> |
} |
332 |
> |
#ifdef IS_MPI |
333 |
|
tempEx = exI; |
334 |
< |
exI = exJ; |
335 |
< |
exJ = tempEx; |
334 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 |
> |
tempEx = exJ; |
336 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
337 |
> |
|
338 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 |
> |
#else // isn't MPI |
340 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 |
> |
#endif //is_mpi |
342 |
|
} |
343 |
< |
#ifdef IS_MPI |
882 |
< |
tempEx = exI; |
883 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
884 |
< |
tempEx = exJ; |
885 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 |
> |
excludeOffset += molInfo.nBends; |
344 |
|
|
345 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
345 |
> |
for(j=0; j<molInfo.nTorsions; j++){ |
346 |
> |
|
347 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 |
> |
|
353 |
> |
exI = theTorsions[j].a; |
354 |
> |
exJ = theTorsions[j].d; |
355 |
> |
|
356 |
> |
// exclude_I must always be the smaller of the pair |
357 |
> |
if( exI > exJ ){ |
358 |
> |
tempEx = exI; |
359 |
> |
exI = exJ; |
360 |
> |
exJ = tempEx; |
361 |
> |
} |
362 |
> |
#ifdef IS_MPI |
363 |
> |
tempEx = exI; |
364 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 |
> |
tempEx = exJ; |
366 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 |
> |
|
368 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
369 |
|
#else // isn't MPI |
370 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
370 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 |
|
#endif //is_mpi |
372 |
< |
} |
373 |
< |
excludeOffset += info.nBends; |
893 |
< |
|
894 |
< |
for(j=0; j<info.nTorsions; j++){ |
372 |
> |
} |
373 |
> |
excludeOffset += molInfo.nTorsions; |
374 |
|
|
896 |
– |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
897 |
– |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
898 |
– |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
899 |
– |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
900 |
– |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
375 |
|
|
376 |
< |
exI = theTorsions[j].a; |
377 |
< |
exJ = theTorsions[j].d; |
376 |
> |
// send the arrays off to the forceField for init. |
377 |
> |
|
378 |
> |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 |
> |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 |
> |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 |
> |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 |
> |
|
383 |
> |
|
384 |
> |
info[k].molecules[i].initialize( molInfo ); |
385 |
|
|
905 |
– |
// exclude_I must always be the smaller of the pair |
906 |
– |
if( exI > exJ ){ |
907 |
– |
tempEx = exI; |
908 |
– |
exI = exJ; |
909 |
– |
exJ = tempEx; |
910 |
– |
} |
911 |
– |
#ifdef IS_MPI |
912 |
– |
tempEx = exI; |
913 |
– |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
914 |
– |
tempEx = exJ; |
915 |
– |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
386 |
|
|
387 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
388 |
< |
#else // isn't MPI |
389 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
390 |
< |
#endif //is_mpi |
387 |
> |
atomOffset += molInfo.nAtoms; |
388 |
> |
delete[] theBonds; |
389 |
> |
delete[] theBends; |
390 |
> |
delete[] theTorsions; |
391 |
|
} |
922 |
– |
excludeOffset += info.nTorsions; |
923 |
– |
|
924 |
– |
|
925 |
– |
// send the arrays off to the forceField for init. |
926 |
– |
|
927 |
– |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
928 |
– |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
929 |
– |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
930 |
– |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
931 |
– |
|
932 |
– |
|
933 |
– |
the_molecules[i].initialize( info ); |
934 |
– |
atomOffset += info.nAtoms; |
935 |
– |
delete[] theBonds; |
936 |
– |
delete[] theBends; |
937 |
– |
delete[] theTorsions; |
392 |
|
} |
393 |
< |
|
393 |
> |
|
394 |
|
#ifdef IS_MPI |
395 |
|
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
396 |
|
MPIcheckPoint(); |
397 |
|
#endif // is_mpi |
398 |
< |
|
398 |
> |
|
399 |
|
// clean up the forcefield |
400 |
+ |
|
401 |
|
the_ff->calcRcut(); |
402 |
|
the_ff->cleanMe(); |
403 |
< |
|
403 |
> |
|
404 |
|
} |
405 |
|
|
406 |
|
void SimSetup::initFromBass( void ){ |
413 |
|
int n_extra; |
414 |
|
int have_extra, done; |
415 |
|
|
416 |
+ |
double vel[3]; |
417 |
+ |
vel[0] = 0.0; |
418 |
+ |
vel[1] = 0.0; |
419 |
+ |
vel[2] = 0.0; |
420 |
+ |
|
421 |
|
temp1 = (double)tot_nmol / 4.0; |
422 |
|
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
423 |
|
temp3 = ceil( temp2 ); |
427 |
|
have_extra =1; |
428 |
|
|
429 |
|
n_cells = (int)temp3 - 1; |
430 |
< |
cellx = simnfo->box_x / temp3; |
431 |
< |
celly = simnfo->box_y / temp3; |
432 |
< |
cellz = simnfo->box_z / temp3; |
430 |
> |
cellx = info[0].boxL[0] / temp3; |
431 |
> |
celly = info[0].boxL[1] / temp3; |
432 |
> |
cellz = info[0].boxL[2] / temp3; |
433 |
|
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
434 |
|
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
435 |
|
n_per_extra = (int)ceil( temp1 ); |
444 |
|
} |
445 |
|
else{ |
446 |
|
n_cells = (int)temp3; |
447 |
< |
cellx = simnfo->box_x / temp3; |
448 |
< |
celly = simnfo->box_y / temp3; |
449 |
< |
cellz = simnfo->box_z / temp3; |
447 |
> |
cellx = info[0].boxL[0] / temp3; |
448 |
> |
celly = info[0].boxL[1] / temp3; |
449 |
> |
cellz = info[0].boxL[2] / temp3; |
450 |
|
} |
451 |
|
|
452 |
|
current_mol = 0; |
525 |
|
} |
526 |
|
} |
527 |
|
|
528 |
< |
|
529 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1070 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
1071 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
1072 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
528 |
> |
for( i=0; i<info[0].n_atoms; i++ ){ |
529 |
> |
info[0].atoms[i]->setVel( vel ); |
530 |
|
} |
531 |
|
} |
532 |
|
|
536 |
|
AtomStamp* current_atom; |
537 |
|
DirectionalAtom* dAtom; |
538 |
|
double rotMat[3][3]; |
539 |
+ |
double pos[3]; |
540 |
|
|
541 |
|
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
542 |
|
|
552 |
|
painCave.isFatal = 1; |
553 |
|
simError(); |
554 |
|
} |
555 |
+ |
|
556 |
+ |
pos[0] = x + current_atom->getPosX(); |
557 |
+ |
pos[1] = y + current_atom->getPosY(); |
558 |
+ |
pos[2] = z + current_atom->getPosZ(); |
559 |
+ |
|
560 |
+ |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
561 |
|
|
562 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1099 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1100 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
562 |
> |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
563 |
|
|
564 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
564 |
> |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
565 |
|
|
1104 |
– |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1105 |
– |
|
566 |
|
rotMat[0][0] = 1.0; |
567 |
|
rotMat[0][1] = 0.0; |
568 |
|
rotMat[0][2] = 0.0; |
588 |
|
|
589 |
|
current_comp_mol = 0; |
590 |
|
current_comp++; |
591 |
+ |
} |
592 |
+ |
} |
593 |
+ |
|
594 |
+ |
|
595 |
+ |
void SimSetup::gatherInfo( void ){ |
596 |
+ |
int i,j,k; |
597 |
+ |
|
598 |
+ |
ensembleCase = -1; |
599 |
+ |
ffCase = -1; |
600 |
+ |
|
601 |
+ |
// set the easy ones first |
602 |
+ |
|
603 |
+ |
for( i=0; i<nInfo; i++){ |
604 |
+ |
info[i].target_temp = globals->getTargetTemp(); |
605 |
+ |
info[i].dt = globals->getDt(); |
606 |
+ |
info[i].run_time = globals->getRunTime(); |
607 |
+ |
} |
608 |
+ |
n_components = globals->getNComponents(); |
609 |
+ |
|
610 |
+ |
|
611 |
+ |
// get the forceField |
612 |
+ |
|
613 |
+ |
strcpy( force_field, globals->getForceField() ); |
614 |
+ |
|
615 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
616 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
617 |
+ |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
618 |
+ |
else{ |
619 |
+ |
sprintf( painCave.errMsg, |
620 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
621 |
+ |
force_field ); |
622 |
+ |
painCave.isFatal = 1; |
623 |
+ |
simError(); |
624 |
+ |
} |
625 |
+ |
|
626 |
+ |
// get the ensemble |
627 |
+ |
|
628 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
629 |
+ |
|
630 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
631 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
632 |
+ |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
633 |
+ |
ensembleCase = NPTi_ENS; |
634 |
+ |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
635 |
+ |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
636 |
+ |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
637 |
+ |
else{ |
638 |
+ |
sprintf( painCave.errMsg, |
639 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 |
+ |
"reverting to NVE for this simulation.\n", |
641 |
+ |
ensemble ); |
642 |
+ |
painCave.isFatal = 0; |
643 |
+ |
simError(); |
644 |
+ |
strcpy( ensemble, "NVE" ); |
645 |
+ |
ensembleCase = NVE_ENS; |
646 |
+ |
} |
647 |
+ |
|
648 |
+ |
for(i=0; i<nInfo; i++){ |
649 |
+ |
|
650 |
+ |
strcpy( info[i].ensemble, ensemble ); |
651 |
+ |
|
652 |
+ |
// get the mixing rule |
653 |
+ |
|
654 |
+ |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
655 |
+ |
info[i].usePBC = globals->getPBC(); |
656 |
+ |
} |
657 |
+ |
|
658 |
+ |
// get the components and calculate the tot_nMol and indvidual n_mol |
659 |
+ |
|
660 |
+ |
the_components = globals->getComponents(); |
661 |
+ |
components_nmol = new int[n_components]; |
662 |
+ |
|
663 |
+ |
|
664 |
+ |
if( !globals->haveNMol() ){ |
665 |
+ |
// we don't have the total number of molecules, so we assume it is |
666 |
+ |
// given in each component |
667 |
+ |
|
668 |
+ |
tot_nmol = 0; |
669 |
+ |
for( i=0; i<n_components; i++ ){ |
670 |
+ |
|
671 |
+ |
if( !the_components[i]->haveNMol() ){ |
672 |
+ |
// we have a problem |
673 |
+ |
sprintf( painCave.errMsg, |
674 |
+ |
"SimSetup Error. No global NMol or component NMol" |
675 |
+ |
" given. Cannot calculate the number of atoms.\n" ); |
676 |
+ |
painCave.isFatal = 1; |
677 |
+ |
simError(); |
678 |
+ |
} |
679 |
+ |
|
680 |
+ |
tot_nmol += the_components[i]->getNMol(); |
681 |
+ |
components_nmol[i] = the_components[i]->getNMol(); |
682 |
+ |
} |
683 |
+ |
} |
684 |
+ |
else{ |
685 |
+ |
sprintf( painCave.errMsg, |
686 |
+ |
"SimSetup error.\n" |
687 |
+ |
"\tSorry, the ability to specify total" |
688 |
+ |
" nMols and then give molfractions in the components\n" |
689 |
+ |
"\tis not currently supported." |
690 |
+ |
" Please give nMol in the components.\n" ); |
691 |
+ |
painCave.isFatal = 1; |
692 |
+ |
simError(); |
693 |
+ |
} |
694 |
+ |
|
695 |
+ |
// set the status, sample, and thermal kick times |
696 |
+ |
|
697 |
+ |
for(i=0; i<nInfo; i++){ |
698 |
+ |
|
699 |
+ |
if( globals->haveSampleTime() ){ |
700 |
+ |
info[i].sampleTime = globals->getSampleTime(); |
701 |
+ |
info[i].statusTime = info[i].sampleTime; |
702 |
+ |
info[i].thermalTime = info[i].sampleTime; |
703 |
+ |
} |
704 |
+ |
else{ |
705 |
+ |
info[i].sampleTime = globals->getRunTime(); |
706 |
+ |
info[i].statusTime = info[i].sampleTime; |
707 |
+ |
info[i].thermalTime = info[i].sampleTime; |
708 |
+ |
} |
709 |
+ |
|
710 |
+ |
if( globals->haveStatusTime() ){ |
711 |
+ |
info[i].statusTime = globals->getStatusTime(); |
712 |
+ |
} |
713 |
+ |
|
714 |
+ |
if( globals->haveThermalTime() ){ |
715 |
+ |
info[i].thermalTime = globals->getThermalTime(); |
716 |
+ |
} |
717 |
+ |
|
718 |
+ |
// check for the temperature set flag |
719 |
+ |
|
720 |
+ |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
721 |
+ |
|
722 |
+ |
// get some of the tricky things that may still be in the globals |
723 |
+ |
|
724 |
+ |
double boxVector[3]; |
725 |
+ |
if( globals->haveBox() ){ |
726 |
+ |
boxVector[0] = globals->getBox(); |
727 |
+ |
boxVector[1] = globals->getBox(); |
728 |
+ |
boxVector[2] = globals->getBox(); |
729 |
+ |
|
730 |
+ |
info[i].setBox( boxVector ); |
731 |
+ |
} |
732 |
+ |
else if( globals->haveDensity() ){ |
733 |
+ |
|
734 |
+ |
double vol; |
735 |
+ |
vol = (double)tot_nmol / globals->getDensity(); |
736 |
+ |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 |
+ |
boxVector[1] = boxVector[0]; |
738 |
+ |
boxVector[2] = boxVector[0]; |
739 |
+ |
|
740 |
+ |
info[i].setBox( boxVector ); |
741 |
+ |
} |
742 |
+ |
else{ |
743 |
+ |
if( !globals->haveBoxX() ){ |
744 |
+ |
sprintf( painCave.errMsg, |
745 |
+ |
"SimSetup error, no periodic BoxX size given.\n" ); |
746 |
+ |
painCave.isFatal = 1; |
747 |
+ |
simError(); |
748 |
+ |
} |
749 |
+ |
boxVector[0] = globals->getBoxX(); |
750 |
+ |
|
751 |
+ |
if( !globals->haveBoxY() ){ |
752 |
+ |
sprintf( painCave.errMsg, |
753 |
+ |
"SimSetup error, no periodic BoxY size given.\n" ); |
754 |
+ |
painCave.isFatal = 1; |
755 |
+ |
simError(); |
756 |
+ |
} |
757 |
+ |
boxVector[1] = globals->getBoxY(); |
758 |
+ |
|
759 |
+ |
if( !globals->haveBoxZ() ){ |
760 |
+ |
sprintf( painCave.errMsg, |
761 |
+ |
"SimSetup error, no periodic BoxZ size given.\n" ); |
762 |
+ |
painCave.isFatal = 1; |
763 |
+ |
simError(); |
764 |
+ |
} |
765 |
+ |
boxVector[2] = globals->getBoxZ(); |
766 |
+ |
|
767 |
+ |
info[i].setBox( boxVector ); |
768 |
+ |
} |
769 |
+ |
|
770 |
+ |
} |
771 |
+ |
|
772 |
+ |
#ifdef IS_MPI |
773 |
+ |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
774 |
+ |
MPIcheckPoint(); |
775 |
+ |
#endif // is_mpi |
776 |
+ |
|
777 |
+ |
} |
778 |
+ |
|
779 |
+ |
|
780 |
+ |
void SimSetup::finalInfoCheck( void ){ |
781 |
+ |
int index; |
782 |
+ |
int usesDipoles; |
783 |
+ |
int i; |
784 |
+ |
|
785 |
+ |
for(i=0; i<nInfo; i++){ |
786 |
+ |
// check electrostatic parameters |
787 |
+ |
|
788 |
+ |
index = 0; |
789 |
+ |
usesDipoles = 0; |
790 |
+ |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
791 |
+ |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
792 |
+ |
index++; |
793 |
+ |
} |
794 |
+ |
|
795 |
+ |
#ifdef IS_MPI |
796 |
+ |
int myUse = usesDipoles; |
797 |
+ |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
798 |
+ |
#endif //is_mpi |
799 |
+ |
|
800 |
+ |
double theEcr, theEst; |
801 |
+ |
|
802 |
+ |
if (globals->getUseRF() ) { |
803 |
+ |
info[i].useReactionField = 1; |
804 |
+ |
|
805 |
+ |
if( !globals->haveECR() ){ |
806 |
+ |
sprintf( painCave.errMsg, |
807 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
808 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
809 |
+ |
"I hope you have a very fast processor!\n"); |
810 |
+ |
painCave.isFatal = 0; |
811 |
+ |
simError(); |
812 |
+ |
double smallest; |
813 |
+ |
smallest = info[i].boxL[0]; |
814 |
+ |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 |
+ |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 |
+ |
theEcr = 0.5 * smallest; |
817 |
+ |
} else { |
818 |
+ |
theEcr = globals->getECR(); |
819 |
+ |
} |
820 |
+ |
|
821 |
+ |
if( !globals->haveEST() ){ |
822 |
+ |
sprintf( painCave.errMsg, |
823 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
824 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 |
+ |
); |
826 |
+ |
painCave.isFatal = 0; |
827 |
+ |
simError(); |
828 |
+ |
theEst = 0.05 * theEcr; |
829 |
+ |
} else { |
830 |
+ |
theEst= globals->getEST(); |
831 |
+ |
} |
832 |
+ |
|
833 |
+ |
info[i].setEcr( theEcr, theEst ); |
834 |
+ |
|
835 |
+ |
if(!globals->haveDielectric() ){ |
836 |
+ |
sprintf( painCave.errMsg, |
837 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
838 |
+ |
"setting a dielectric constant!\n" |
839 |
+ |
); |
840 |
+ |
painCave.isFatal = 1; |
841 |
+ |
simError(); |
842 |
+ |
} |
843 |
+ |
info[i].dielectric = globals->getDielectric(); |
844 |
+ |
} |
845 |
+ |
else { |
846 |
+ |
if (usesDipoles) { |
847 |
+ |
|
848 |
+ |
if( !globals->haveECR() ){ |
849 |
+ |
sprintf( painCave.errMsg, |
850 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
851 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
852 |
+ |
"I hope you have a very fast processor!\n"); |
853 |
+ |
painCave.isFatal = 0; |
854 |
+ |
simError(); |
855 |
+ |
double smallest; |
856 |
+ |
smallest = info[i].boxL[0]; |
857 |
+ |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 |
+ |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 |
+ |
theEcr = 0.5 * smallest; |
860 |
+ |
} else { |
861 |
+ |
theEcr = globals->getECR(); |
862 |
+ |
} |
863 |
+ |
|
864 |
+ |
if( !globals->haveEST() ){ |
865 |
+ |
sprintf( painCave.errMsg, |
866 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
867 |
+ |
"electrostaticCutoffRadius for the " |
868 |
+ |
"electrostaticSkinThickness\n" |
869 |
+ |
); |
870 |
+ |
painCave.isFatal = 0; |
871 |
+ |
simError(); |
872 |
+ |
theEst = 0.05 * theEcr; |
873 |
+ |
} else { |
874 |
+ |
theEst= globals->getEST(); |
875 |
+ |
} |
876 |
+ |
|
877 |
+ |
info[i].setEcr( theEcr, theEst ); |
878 |
+ |
} |
879 |
+ |
} |
880 |
+ |
} |
881 |
+ |
|
882 |
+ |
#ifdef IS_MPI |
883 |
+ |
strcpy( checkPointMsg, "post processing checks out" ); |
884 |
+ |
MPIcheckPoint(); |
885 |
+ |
#endif // is_mpi |
886 |
+ |
|
887 |
+ |
} |
888 |
+ |
|
889 |
+ |
void SimSetup::initSystemCoords( void ){ |
890 |
+ |
int i; |
891 |
+ |
|
892 |
+ |
char* inName; |
893 |
+ |
|
894 |
+ |
|
895 |
+ |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
896 |
+ |
|
897 |
+ |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
898 |
+ |
|
899 |
+ |
if( globals->haveInitialConfig() ){ |
900 |
+ |
|
901 |
+ |
InitializeFromFile* fileInit; |
902 |
+ |
#ifdef IS_MPI // is_mpi |
903 |
+ |
if( worldRank == 0 ){ |
904 |
+ |
#endif //is_mpi |
905 |
+ |
inName = globals->getInitialConfig(); |
906 |
+ |
double* tempDouble = new double[1000000]; |
907 |
+ |
fileInit = new InitializeFromFile( inName ); |
908 |
+ |
#ifdef IS_MPI |
909 |
+ |
}else fileInit = new InitializeFromFile( NULL ); |
910 |
+ |
#endif |
911 |
+ |
fileInit->readInit( info ); // default velocities on |
912 |
+ |
|
913 |
+ |
delete fileInit; |
914 |
+ |
} |
915 |
+ |
else{ |
916 |
+ |
|
917 |
+ |
#ifdef IS_MPI |
918 |
+ |
|
919 |
+ |
// no init from bass |
920 |
+ |
|
921 |
+ |
sprintf( painCave.errMsg, |
922 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
923 |
+ |
painCave.isFatal; |
924 |
+ |
simError(); |
925 |
+ |
|
926 |
+ |
#else |
927 |
+ |
|
928 |
+ |
initFromBass(); |
929 |
+ |
|
930 |
+ |
|
931 |
+ |
#endif |
932 |
+ |
} |
933 |
+ |
|
934 |
+ |
#ifdef IS_MPI |
935 |
+ |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
936 |
+ |
MPIcheckPoint(); |
937 |
+ |
#endif // is_mpi |
938 |
+ |
|
939 |
+ |
} |
940 |
+ |
|
941 |
+ |
|
942 |
+ |
void SimSetup::makeOutNames( void ){ |
943 |
+ |
|
944 |
+ |
int k; |
945 |
+ |
|
946 |
+ |
|
947 |
+ |
for(k=0; k<nInfo; k++){ |
948 |
+ |
|
949 |
+ |
#ifdef IS_MPI |
950 |
+ |
if( worldRank == 0 ){ |
951 |
+ |
#endif // is_mpi |
952 |
+ |
|
953 |
+ |
if( globals->haveFinalConfig() ){ |
954 |
+ |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
955 |
+ |
} |
956 |
+ |
else{ |
957 |
+ |
strcpy( info[k].finalName, inFileName ); |
958 |
+ |
char* endTest; |
959 |
+ |
int nameLength = strlen( info[k].finalName ); |
960 |
+ |
endTest = &(info[k].finalName[nameLength - 5]); |
961 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
962 |
+ |
strcpy( endTest, ".eor" ); |
963 |
+ |
} |
964 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
965 |
+ |
strcpy( endTest, ".eor" ); |
966 |
+ |
} |
967 |
+ |
else{ |
968 |
+ |
endTest = &(info[k].finalName[nameLength - 4]); |
969 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
970 |
+ |
strcpy( endTest, ".eor" ); |
971 |
+ |
} |
972 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
973 |
+ |
strcpy( endTest, ".eor" ); |
974 |
+ |
} |
975 |
+ |
else{ |
976 |
+ |
strcat( info[k].finalName, ".eor" ); |
977 |
+ |
} |
978 |
+ |
} |
979 |
+ |
} |
980 |
+ |
|
981 |
+ |
// make the sample and status out names |
982 |
+ |
|
983 |
+ |
strcpy( info[k].sampleName, inFileName ); |
984 |
+ |
char* endTest; |
985 |
+ |
int nameLength = strlen( info[k].sampleName ); |
986 |
+ |
endTest = &(info[k].sampleName[nameLength - 5]); |
987 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
988 |
+ |
strcpy( endTest, ".dump" ); |
989 |
+ |
} |
990 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
991 |
+ |
strcpy( endTest, ".dump" ); |
992 |
+ |
} |
993 |
+ |
else{ |
994 |
+ |
endTest = &(info[k].sampleName[nameLength - 4]); |
995 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
996 |
+ |
strcpy( endTest, ".dump" ); |
997 |
+ |
} |
998 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
999 |
+ |
strcpy( endTest, ".dump" ); |
1000 |
+ |
} |
1001 |
+ |
else{ |
1002 |
+ |
strcat( info[k].sampleName, ".dump" ); |
1003 |
+ |
} |
1004 |
+ |
} |
1005 |
+ |
|
1006 |
+ |
strcpy( info[k].statusName, inFileName ); |
1007 |
+ |
nameLength = strlen( info[k].statusName ); |
1008 |
+ |
endTest = &(info[k].statusName[nameLength - 5]); |
1009 |
+ |
if( !strcmp( endTest, ".bass" ) ){ |
1010 |
+ |
strcpy( endTest, ".stat" ); |
1011 |
+ |
} |
1012 |
+ |
else if( !strcmp( endTest, ".BASS" ) ){ |
1013 |
+ |
strcpy( endTest, ".stat" ); |
1014 |
+ |
} |
1015 |
+ |
else{ |
1016 |
+ |
endTest = &(info[k].statusName[nameLength - 4]); |
1017 |
+ |
if( !strcmp( endTest, ".bss" ) ){ |
1018 |
+ |
strcpy( endTest, ".stat" ); |
1019 |
+ |
} |
1020 |
+ |
else if( !strcmp( endTest, ".mdl" ) ){ |
1021 |
+ |
strcpy( endTest, ".stat" ); |
1022 |
+ |
} |
1023 |
+ |
else{ |
1024 |
+ |
strcat( info[k].statusName, ".stat" ); |
1025 |
+ |
} |
1026 |
+ |
} |
1027 |
+ |
|
1028 |
+ |
#ifdef IS_MPI |
1029 |
+ |
} |
1030 |
+ |
#endif // is_mpi |
1031 |
+ |
} |
1032 |
+ |
} |
1033 |
+ |
|
1034 |
+ |
|
1035 |
+ |
void SimSetup::sysObjectsCreation( void ){ |
1036 |
+ |
|
1037 |
+ |
int i,k; |
1038 |
+ |
|
1039 |
+ |
// create the forceField |
1040 |
+ |
|
1041 |
+ |
createFF(); |
1042 |
+ |
|
1043 |
+ |
// extract componentList |
1044 |
+ |
|
1045 |
+ |
compList(); |
1046 |
+ |
|
1047 |
+ |
// calc the number of atoms, bond, bends, and torsions |
1048 |
+ |
|
1049 |
+ |
calcSysValues(); |
1050 |
+ |
|
1051 |
+ |
#ifdef IS_MPI |
1052 |
+ |
// divide the molecules among the processors |
1053 |
+ |
|
1054 |
+ |
mpiMolDivide(); |
1055 |
+ |
#endif //is_mpi |
1056 |
+ |
|
1057 |
+ |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1058 |
+ |
|
1059 |
+ |
makeSysArrays(); |
1060 |
+ |
|
1061 |
+ |
// make and initialize the molecules (all but atomic coordinates) |
1062 |
+ |
|
1063 |
+ |
makeMolecules(); |
1064 |
+ |
|
1065 |
+ |
for(k=0; k<nInfo; k++){ |
1066 |
+ |
info[k].identArray = new int[info[k].n_atoms]; |
1067 |
+ |
for(i=0; i<info[k].n_atoms; i++){ |
1068 |
+ |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1069 |
+ |
} |
1070 |
+ |
} |
1071 |
+ |
} |
1072 |
+ |
|
1073 |
+ |
|
1074 |
+ |
void SimSetup::createFF( void ){ |
1075 |
+ |
|
1076 |
+ |
switch( ffCase ){ |
1077 |
+ |
|
1078 |
+ |
case FF_DUFF: |
1079 |
+ |
the_ff = new DUFF(); |
1080 |
+ |
break; |
1081 |
+ |
|
1082 |
+ |
case FF_LJ: |
1083 |
+ |
the_ff = new LJFF(); |
1084 |
+ |
break; |
1085 |
+ |
|
1086 |
+ |
case FF_EAM: |
1087 |
+ |
the_ff = new EAM_FF(); |
1088 |
+ |
break; |
1089 |
+ |
|
1090 |
+ |
default: |
1091 |
+ |
sprintf( painCave.errMsg, |
1092 |
+ |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1093 |
+ |
painCave.isFatal = 1; |
1094 |
+ |
simError(); |
1095 |
+ |
} |
1096 |
+ |
|
1097 |
+ |
#ifdef IS_MPI |
1098 |
+ |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1099 |
+ |
MPIcheckPoint(); |
1100 |
+ |
#endif // is_mpi |
1101 |
+ |
|
1102 |
+ |
} |
1103 |
+ |
|
1104 |
+ |
|
1105 |
+ |
void SimSetup::compList( void ){ |
1106 |
+ |
|
1107 |
+ |
int i; |
1108 |
+ |
char* id; |
1109 |
+ |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1110 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1111 |
+ |
comp_stamps = new MoleculeStamp*[n_components]; |
1112 |
+ |
|
1113 |
+ |
// make an array of molecule stamps that match the components used. |
1114 |
+ |
// also extract the used stamps out into a separate linked list |
1115 |
+ |
|
1116 |
+ |
for(i=0; i<nInfo; i++){ |
1117 |
+ |
info[i].nComponents = n_components; |
1118 |
+ |
info[i].componentsNmol = components_nmol; |
1119 |
+ |
info[i].compStamps = comp_stamps; |
1120 |
+ |
info[i].headStamp = headStamp; |
1121 |
+ |
} |
1122 |
+ |
|
1123 |
+ |
|
1124 |
+ |
for( i=0; i<n_components; i++ ){ |
1125 |
+ |
|
1126 |
+ |
id = the_components[i]->getType(); |
1127 |
+ |
comp_stamps[i] = NULL; |
1128 |
+ |
|
1129 |
+ |
// check to make sure the component isn't already in the list |
1130 |
+ |
|
1131 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1132 |
+ |
if( comp_stamps[i] == NULL ){ |
1133 |
+ |
|
1134 |
+ |
// extract the component from the list; |
1135 |
+ |
|
1136 |
+ |
currentStamp = stamps->extractMolStamp( id ); |
1137 |
+ |
if( currentStamp == NULL ){ |
1138 |
+ |
sprintf( painCave.errMsg, |
1139 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1140 |
+ |
"list of declared molecules\n", |
1141 |
+ |
id ); |
1142 |
+ |
painCave.isFatal = 1; |
1143 |
+ |
simError(); |
1144 |
+ |
} |
1145 |
+ |
|
1146 |
+ |
headStamp->add( currentStamp ); |
1147 |
+ |
comp_stamps[i] = headStamp->match( id ); |
1148 |
+ |
} |
1149 |
+ |
} |
1150 |
+ |
|
1151 |
+ |
#ifdef IS_MPI |
1152 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1153 |
+ |
MPIcheckPoint(); |
1154 |
+ |
#endif // is_mpi |
1155 |
+ |
|
1156 |
+ |
|
1157 |
+ |
} |
1158 |
+ |
|
1159 |
+ |
void SimSetup::calcSysValues( void ){ |
1160 |
+ |
int i, j, k; |
1161 |
+ |
|
1162 |
+ |
int *molMembershipArray; |
1163 |
+ |
|
1164 |
+ |
tot_atoms = 0; |
1165 |
+ |
tot_bonds = 0; |
1166 |
+ |
tot_bends = 0; |
1167 |
+ |
tot_torsions = 0; |
1168 |
+ |
for( i=0; i<n_components; i++ ){ |
1169 |
+ |
|
1170 |
+ |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1171 |
+ |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1172 |
+ |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1173 |
+ |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1174 |
+ |
} |
1175 |
+ |
|
1176 |
+ |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1177 |
+ |
molMembershipArray = new int[tot_atoms]; |
1178 |
+ |
|
1179 |
+ |
for(i=0; i<nInfo; i++){ |
1180 |
+ |
info[i].n_atoms = tot_atoms; |
1181 |
+ |
info[i].n_bonds = tot_bonds; |
1182 |
+ |
info[i].n_bends = tot_bends; |
1183 |
+ |
info[i].n_torsions = tot_torsions; |
1184 |
+ |
info[i].n_SRI = tot_SRI; |
1185 |
+ |
info[i].n_mol = tot_nmol; |
1186 |
+ |
|
1187 |
+ |
info[i].molMembershipArray = molMembershipArray; |
1188 |
+ |
} |
1189 |
+ |
} |
1190 |
+ |
|
1191 |
+ |
#ifdef IS_MPI |
1192 |
+ |
|
1193 |
+ |
void SimSetup::mpiMolDivide( void ){ |
1194 |
+ |
|
1195 |
+ |
int i, j, k; |
1196 |
+ |
int localMol, allMol; |
1197 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1198 |
+ |
|
1199 |
+ |
mpiSim = new mpiSimulation( info ); |
1200 |
+ |
|
1201 |
+ |
globalIndex = mpiSim->divideLabor(); |
1202 |
+ |
|
1203 |
+ |
// set up the local variables |
1204 |
+ |
|
1205 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1206 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1207 |
+ |
|
1208 |
+ |
allMol = 0; |
1209 |
+ |
localMol = 0; |
1210 |
+ |
local_atoms = 0; |
1211 |
+ |
local_bonds = 0; |
1212 |
+ |
local_bends = 0; |
1213 |
+ |
local_torsions = 0; |
1214 |
+ |
globalAtomIndex = 0; |
1215 |
+ |
|
1216 |
+ |
|
1217 |
+ |
for( i=0; i<n_components; i++ ){ |
1218 |
+ |
|
1219 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1220 |
+ |
|
1221 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1222 |
+ |
|
1223 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1224 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1225 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1226 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1227 |
+ |
localMol++; |
1228 |
+ |
} |
1229 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1230 |
+ |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1231 |
+ |
globalAtomIndex++; |
1232 |
+ |
} |
1233 |
+ |
|
1234 |
+ |
allMol++; |
1235 |
+ |
} |
1236 |
+ |
} |
1237 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1238 |
+ |
|
1239 |
+ |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1240 |
+ |
|
1241 |
+ |
if( local_atoms != info[0].n_atoms ){ |
1242 |
+ |
sprintf( painCave.errMsg, |
1243 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1244 |
+ |
" localAtom (%d) are not equal.\n", |
1245 |
+ |
info[0].n_atoms, |
1246 |
+ |
local_atoms ); |
1247 |
+ |
painCave.isFatal = 1; |
1248 |
+ |
simError(); |
1249 |
+ |
} |
1250 |
+ |
|
1251 |
+ |
info[0].n_bonds = local_bonds; |
1252 |
+ |
info[0].n_bends = local_bends; |
1253 |
+ |
info[0].n_torsions = local_torsions; |
1254 |
+ |
info[0].n_SRI = local_SRI; |
1255 |
+ |
info[0].n_mol = localMol; |
1256 |
+ |
|
1257 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1258 |
+ |
MPIcheckPoint(); |
1259 |
+ |
} |
1260 |
+ |
|
1261 |
+ |
#endif // is_mpi |
1262 |
+ |
|
1263 |
+ |
|
1264 |
+ |
void SimSetup::makeSysArrays( void ){ |
1265 |
+ |
int i, j, k, l; |
1266 |
+ |
|
1267 |
+ |
Atom** the_atoms; |
1268 |
+ |
Molecule* the_molecules; |
1269 |
+ |
Exclude** the_excludes; |
1270 |
+ |
|
1271 |
+ |
|
1272 |
+ |
for(l=0; l<nInfo; l++){ |
1273 |
+ |
|
1274 |
+ |
// create the atom and short range interaction arrays |
1275 |
+ |
|
1276 |
+ |
the_atoms = new Atom*[info[l].n_atoms]; |
1277 |
+ |
the_molecules = new Molecule[info[l].n_mol]; |
1278 |
+ |
int molIndex; |
1279 |
+ |
|
1280 |
+ |
// initialize the molecule's stampID's |
1281 |
+ |
|
1282 |
+ |
#ifdef IS_MPI |
1283 |
+ |
|
1284 |
+ |
|
1285 |
+ |
molIndex = 0; |
1286 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1287 |
+ |
|
1288 |
+ |
if(mol2proc[i] == worldRank ){ |
1289 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1290 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1291 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
1292 |
+ |
molIndex++; |
1293 |
+ |
} |
1294 |
+ |
} |
1295 |
+ |
|
1296 |
+ |
#else // is_mpi |
1297 |
+ |
|
1298 |
+ |
molIndex = 0; |
1299 |
+ |
globalAtomIndex = 0; |
1300 |
+ |
for(i=0; i<n_components; i++){ |
1301 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1302 |
+ |
the_molecules[molIndex].setStampID( i ); |
1303 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1304 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1305 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1306 |
+ |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1307 |
+ |
globalAtomIndex++; |
1308 |
+ |
} |
1309 |
+ |
molIndex++; |
1310 |
+ |
} |
1311 |
+ |
} |
1312 |
+ |
|
1313 |
+ |
|
1314 |
+ |
#endif // is_mpi |
1315 |
+ |
|
1316 |
+ |
|
1317 |
+ |
if( info[l].n_SRI ){ |
1318 |
+ |
|
1319 |
+ |
Exclude::createArray(info[l].n_SRI); |
1320 |
+ |
the_excludes = new Exclude*[info[l].n_SRI]; |
1321 |
+ |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1322 |
+ |
the_excludes[ex] = new Exclude(ex); |
1323 |
+ |
} |
1324 |
+ |
info[l].globalExcludes = new int; |
1325 |
+ |
info[l].n_exclude = info[l].n_SRI; |
1326 |
+ |
} |
1327 |
+ |
else{ |
1328 |
+ |
|
1329 |
+ |
Exclude::createArray( 1 ); |
1330 |
+ |
the_excludes = new Exclude*; |
1331 |
+ |
the_excludes[0] = new Exclude(0); |
1332 |
+ |
the_excludes[0]->setPair( 0,0 ); |
1333 |
+ |
info[l].globalExcludes = new int; |
1334 |
+ |
info[l].globalExcludes[0] = 0; |
1335 |
+ |
info[l].n_exclude = 0; |
1336 |
+ |
} |
1337 |
+ |
|
1338 |
+ |
// set the arrays into the SimInfo object |
1339 |
+ |
|
1340 |
+ |
info[l].atoms = the_atoms; |
1341 |
+ |
info[l].molecules = the_molecules; |
1342 |
+ |
info[l].nGlobalExcludes = 0; |
1343 |
+ |
info[l].excludes = the_excludes; |
1344 |
+ |
|
1345 |
+ |
the_ff->setSimInfo( info ); |
1346 |
+ |
|
1347 |
+ |
} |
1348 |
+ |
} |
1349 |
+ |
|
1350 |
+ |
void SimSetup::makeIntegrator( void ){ |
1351 |
+ |
|
1352 |
+ |
int k; |
1353 |
+ |
|
1354 |
+ |
NVT<RealIntegrator>* myNVT = NULL; |
1355 |
+ |
NPTi<RealIntegrator>* myNPTi = NULL; |
1356 |
+ |
NPTf<RealIntegrator>* myNPTf = NULL; |
1357 |
+ |
NPTim<RealIntegrator>* myNPTim = NULL; |
1358 |
+ |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1359 |
+ |
|
1360 |
+ |
for(k=0; k<nInfo; k++){ |
1361 |
+ |
|
1362 |
+ |
switch( ensembleCase ){ |
1363 |
+ |
|
1364 |
+ |
case NVE_ENS: |
1365 |
+ |
if (globals->haveZconstraints()){ |
1366 |
+ |
setupZConstraint(info[k]); |
1367 |
+ |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1368 |
+ |
} |
1369 |
+ |
|
1370 |
+ |
else |
1371 |
+ |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1372 |
+ |
break; |
1373 |
+ |
|
1374 |
+ |
case NVT_ENS: |
1375 |
+ |
if (globals->haveZconstraints()){ |
1376 |
+ |
setupZConstraint(info[k]); |
1377 |
+ |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1378 |
+ |
} |
1379 |
+ |
else |
1380 |
+ |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1381 |
+ |
|
1382 |
+ |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1383 |
+ |
|
1384 |
+ |
if (globals->haveTauThermostat()) |
1385 |
+ |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1386 |
+ |
|
1387 |
+ |
else { |
1388 |
+ |
sprintf( painCave.errMsg, |
1389 |
+ |
"SimSetup error: If you use the NVT\n" |
1390 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1391 |
+ |
painCave.isFatal = 1; |
1392 |
+ |
simError(); |
1393 |
+ |
} |
1394 |
+ |
break; |
1395 |
+ |
|
1396 |
+ |
case NPTi_ENS: |
1397 |
+ |
if (globals->haveZconstraints()){ |
1398 |
+ |
setupZConstraint(info[k]); |
1399 |
+ |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1400 |
+ |
} |
1401 |
+ |
else |
1402 |
+ |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1403 |
+ |
|
1404 |
+ |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1405 |
+ |
|
1406 |
+ |
if (globals->haveTargetPressure()) |
1407 |
+ |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1408 |
+ |
else { |
1409 |
+ |
sprintf( painCave.errMsg, |
1410 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1411 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1412 |
+ |
painCave.isFatal = 1; |
1413 |
+ |
simError(); |
1414 |
+ |
} |
1415 |
+ |
|
1416 |
+ |
if( globals->haveTauThermostat() ) |
1417 |
+ |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1418 |
+ |
else{ |
1419 |
+ |
sprintf( painCave.errMsg, |
1420 |
+ |
"SimSetup error: If you use an NPT\n" |
1421 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1422 |
+ |
painCave.isFatal = 1; |
1423 |
+ |
simError(); |
1424 |
+ |
} |
1425 |
+ |
|
1426 |
+ |
if( globals->haveTauBarostat() ) |
1427 |
+ |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1428 |
+ |
else{ |
1429 |
+ |
sprintf( painCave.errMsg, |
1430 |
+ |
"SimSetup error: If you use an NPT\n" |
1431 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1432 |
+ |
painCave.isFatal = 1; |
1433 |
+ |
simError(); |
1434 |
+ |
} |
1435 |
+ |
break; |
1436 |
+ |
|
1437 |
+ |
case NPTf_ENS: |
1438 |
+ |
if (globals->haveZconstraints()){ |
1439 |
+ |
setupZConstraint(info[k]); |
1440 |
+ |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1441 |
+ |
} |
1442 |
+ |
else |
1443 |
+ |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1444 |
+ |
|
1445 |
+ |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1446 |
+ |
|
1447 |
+ |
if (globals->haveTargetPressure()) |
1448 |
+ |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1449 |
+ |
else { |
1450 |
+ |
sprintf( painCave.errMsg, |
1451 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1452 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1453 |
+ |
painCave.isFatal = 1; |
1454 |
+ |
simError(); |
1455 |
+ |
} |
1456 |
+ |
|
1457 |
+ |
if( globals->haveTauThermostat() ) |
1458 |
+ |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1459 |
+ |
else{ |
1460 |
+ |
sprintf( painCave.errMsg, |
1461 |
+ |
"SimSetup error: If you use an NPT\n" |
1462 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1463 |
+ |
painCave.isFatal = 1; |
1464 |
+ |
simError(); |
1465 |
+ |
} |
1466 |
+ |
|
1467 |
+ |
if( globals->haveTauBarostat() ) |
1468 |
+ |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1469 |
+ |
else{ |
1470 |
+ |
sprintf( painCave.errMsg, |
1471 |
+ |
"SimSetup error: If you use an NPT\n" |
1472 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1473 |
+ |
painCave.isFatal = 1; |
1474 |
+ |
simError(); |
1475 |
+ |
} |
1476 |
+ |
break; |
1477 |
+ |
|
1478 |
+ |
case NPTim_ENS: |
1479 |
+ |
if (globals->haveZconstraints()){ |
1480 |
+ |
setupZConstraint(info[k]); |
1481 |
+ |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1482 |
+ |
} |
1483 |
+ |
else |
1484 |
+ |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1485 |
+ |
|
1486 |
+ |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1487 |
+ |
|
1488 |
+ |
if (globals->haveTargetPressure()) |
1489 |
+ |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1490 |
+ |
else { |
1491 |
+ |
sprintf( painCave.errMsg, |
1492 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1493 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1494 |
+ |
painCave.isFatal = 1; |
1495 |
+ |
simError(); |
1496 |
+ |
} |
1497 |
+ |
|
1498 |
+ |
if( globals->haveTauThermostat() ) |
1499 |
+ |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1500 |
+ |
else{ |
1501 |
+ |
sprintf( painCave.errMsg, |
1502 |
+ |
"SimSetup error: If you use an NPT\n" |
1503 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1504 |
+ |
painCave.isFatal = 1; |
1505 |
+ |
simError(); |
1506 |
+ |
} |
1507 |
+ |
|
1508 |
+ |
if( globals->haveTauBarostat() ) |
1509 |
+ |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1510 |
+ |
else{ |
1511 |
+ |
sprintf( painCave.errMsg, |
1512 |
+ |
"SimSetup error: If you use an NPT\n" |
1513 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1514 |
+ |
painCave.isFatal = 1; |
1515 |
+ |
simError(); |
1516 |
+ |
} |
1517 |
+ |
break; |
1518 |
+ |
|
1519 |
+ |
case NPTfm_ENS: |
1520 |
+ |
if (globals->haveZconstraints()){ |
1521 |
+ |
setupZConstraint(info[k]); |
1522 |
+ |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1523 |
+ |
} |
1524 |
+ |
else |
1525 |
+ |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1526 |
+ |
|
1527 |
+ |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1528 |
+ |
|
1529 |
+ |
if (globals->haveTargetPressure()) |
1530 |
+ |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1531 |
+ |
else { |
1532 |
+ |
sprintf( painCave.errMsg, |
1533 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1534 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1535 |
+ |
painCave.isFatal = 1; |
1536 |
+ |
simError(); |
1537 |
+ |
} |
1538 |
+ |
|
1539 |
+ |
if( globals->haveTauThermostat() ) |
1540 |
+ |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1541 |
+ |
else{ |
1542 |
+ |
sprintf( painCave.errMsg, |
1543 |
+ |
"SimSetup error: If you use an NPT\n" |
1544 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1545 |
+ |
painCave.isFatal = 1; |
1546 |
+ |
simError(); |
1547 |
+ |
} |
1548 |
+ |
|
1549 |
+ |
if( globals->haveTauBarostat() ) |
1550 |
+ |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1551 |
+ |
else{ |
1552 |
+ |
sprintf( painCave.errMsg, |
1553 |
+ |
"SimSetup error: If you use an NPT\n" |
1554 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1555 |
+ |
painCave.isFatal = 1; |
1556 |
+ |
simError(); |
1557 |
+ |
} |
1558 |
+ |
break; |
1559 |
+ |
|
1560 |
+ |
default: |
1561 |
+ |
sprintf( painCave.errMsg, |
1562 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1563 |
+ |
painCave.isFatal = 1; |
1564 |
+ |
simError(); |
1565 |
+ |
} |
1566 |
|
} |
1567 |
|
} |
1568 |
+ |
|
1569 |
+ |
void SimSetup::initFortran( void ){ |
1570 |
+ |
|
1571 |
+ |
info[0].refreshSim(); |
1572 |
+ |
|
1573 |
+ |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1574 |
+ |
the_ff->initForceField( LB_MIXING_RULE ); |
1575 |
+ |
} |
1576 |
+ |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1577 |
+ |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1578 |
+ |
} |
1579 |
+ |
else{ |
1580 |
+ |
sprintf( painCave.errMsg, |
1581 |
+ |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1582 |
+ |
info[0].mixingRule ); |
1583 |
+ |
painCave.isFatal = 1; |
1584 |
+ |
simError(); |
1585 |
+ |
} |
1586 |
+ |
|
1587 |
+ |
|
1588 |
+ |
#ifdef IS_MPI |
1589 |
+ |
strcpy( checkPointMsg, |
1590 |
+ |
"Successfully intialized the mixingRule for Fortran." ); |
1591 |
+ |
MPIcheckPoint(); |
1592 |
+ |
#endif // is_mpi |
1593 |
+ |
|
1594 |
+ |
} |
1595 |
+ |
|
1596 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1597 |
+ |
{ |
1598 |
+ |
int nZConstraints; |
1599 |
+ |
ZconStamp** zconStamp; |
1600 |
+ |
|
1601 |
+ |
if(globals->haveZconstraintTime()){ |
1602 |
+ |
|
1603 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1604 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1605 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1606 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1607 |
+ |
theInfo.addProperty(zconsTimeProp); |
1608 |
+ |
} |
1609 |
+ |
else{ |
1610 |
+ |
sprintf( painCave.errMsg, |
1611 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1612 |
+ |
" , you must set sample time.\n"); |
1613 |
+ |
painCave.isFatal = 1; |
1614 |
+ |
simError(); |
1615 |
+ |
} |
1616 |
+ |
|
1617 |
+ |
//push zconsTol into siminfo, if user does not specify |
1618 |
+ |
//value for zconsTol, a default value will be used |
1619 |
+ |
DoubleData* zconsTol = new DoubleData(); |
1620 |
+ |
zconsTol->setID(ZCONSTOL_ID); |
1621 |
+ |
if(globals->haveZconsTol()){ |
1622 |
+ |
zconsTol->setData(globals->getZconsTol()); |
1623 |
+ |
} |
1624 |
+ |
else{ |
1625 |
+ |
double defaultZConsTol = 0.01; |
1626 |
+ |
sprintf( painCave.errMsg, |
1627 |
+ |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1628 |
+ |
" , default value %f is used.\n", defaultZConsTol); |
1629 |
+ |
painCave.isFatal = 0; |
1630 |
+ |
simError(); |
1631 |
+ |
|
1632 |
+ |
zconsTol->setData(defaultZConsTol); |
1633 |
+ |
} |
1634 |
+ |
theInfo.addProperty(zconsTol); |
1635 |
+ |
|
1636 |
+ |
//set Force Substraction Policy |
1637 |
+ |
StringData* zconsForcePolicy = new StringData(); |
1638 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1639 |
+ |
|
1640 |
+ |
if(globals->haveZconsForcePolicy()){ |
1641 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1642 |
+ |
} |
1643 |
+ |
else{ |
1644 |
+ |
sprintf( painCave.errMsg, |
1645 |
+ |
"ZConstraint Warning: User does not set force substraction policy, " |
1646 |
+ |
"average force substraction policy is used\n"); |
1647 |
+ |
painCave.isFatal = 0; |
1648 |
+ |
simError(); |
1649 |
+ |
zconsForcePolicy->setData("BYNUMBER"); |
1650 |
+ |
} |
1651 |
+ |
|
1652 |
+ |
theInfo.addProperty(zconsForcePolicy); |
1653 |
+ |
|
1654 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1655 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1656 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1657 |
+ |
|
1658 |
+ |
string zconsOutput(theInfo.finalName); |
1659 |
+ |
|
1660 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1661 |
+ |
|
1662 |
+ |
StringData* zconsFilename = new StringData(); |
1663 |
+ |
zconsFilename->setID(ZCONSFILENAME_ID); |
1664 |
+ |
zconsFilename->setData(zconsOutput); |
1665 |
+ |
|
1666 |
+ |
theInfo.addProperty(zconsFilename); |
1667 |
+ |
|
1668 |
+ |
//setup index, pos and other parameters of z-constraint molecules |
1669 |
+ |
nZConstraints = globals->getNzConstraints(); |
1670 |
+ |
theInfo.nZconstraints = nZConstraints; |
1671 |
+ |
|
1672 |
+ |
zconStamp = globals->getZconStamp(); |
1673 |
+ |
ZConsParaItem tempParaItem; |
1674 |
+ |
|
1675 |
+ |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1676 |
+ |
zconsParaData->setID(ZCONSPARADATA_ID); |
1677 |
+ |
|
1678 |
+ |
for(int i = 0; i < nZConstraints; i++){ |
1679 |
+ |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1680 |
+ |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1681 |
+ |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1682 |
+ |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1683 |
+ |
|
1684 |
+ |
zconsParaData->addItem(tempParaItem); |
1685 |
+ |
} |
1686 |
+ |
|
1687 |
+ |
//sort the parameters by index of molecules |
1688 |
+ |
zconsParaData->sortByIndex(); |
1689 |
+ |
|
1690 |
+ |
//push data into siminfo, therefore, we can retrieve later |
1691 |
+ |
theInfo.addProperty(zconsParaData); |
1692 |
+ |
|
1693 |
+ |
} |