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#include <cstdlib> |
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#include <algorithm> |
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#include <stdlib.h> |
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#include <iostream> |
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#include <cmath> |
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|
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#include <math.h> |
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#include <string> |
6 |
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#include <sprng.h> |
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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 NPTxyz_ENS 4 |
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|
26 |
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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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|
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SimSetup::SimSetup(){ |
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|
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initSuspend = false; |
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isInfoArray = 0; |
37 |
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nInfo = 1; |
38 |
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|
39 |
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stamps = new MakeStamps(); |
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globals = new Globals(); |
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|
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|
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|
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#ifdef IS_MPI |
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strcpy( checkPointMsg, "SimSetup creation successful" ); |
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strcpy(checkPointMsg, "SimSetup creation successful"); |
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MPIcheckPoint(); |
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#endif // IS_MPI |
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} |
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delete globals; |
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} |
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|
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void SimSetup::parseFile( char* fileName ){ |
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void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
55 |
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info = the_info; |
56 |
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nInfo = theNinfo; |
57 |
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isInfoArray = 1; |
58 |
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initSuspend = true; |
59 |
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} |
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|
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|
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void SimSetup::parseFile(char* fileName){ |
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#ifdef IS_MPI |
64 |
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if( worldRank == 0 ){ |
64 |
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if (worldRank == 0){ |
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#endif // is_mpi |
66 |
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|
66 |
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|
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inFileName = fileName; |
68 |
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set_interface_stamps( stamps, globals ); |
69 |
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|
68 |
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set_interface_stamps(stamps, globals); |
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|
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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|
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yacc_BASS( fileName ); |
74 |
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yacc_BASS(fileName); |
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|
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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else receiveParse(); |
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else{ |
80 |
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receiveParse(); |
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} |
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#endif |
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|
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} |
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|
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#ifdef IS_MPI |
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void SimSetup::receiveParse(void){ |
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|
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set_interface_stamps( stamps, globals ); |
90 |
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mpiEventInit(); |
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MPIcheckPoint(); |
59 |
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mpiEventLoop(); |
60 |
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|
88 |
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set_interface_stamps(stamps, globals); |
89 |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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|
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#endif // is_mpi |
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|
96 |
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void SimSetup::createSim( void ){ |
96 |
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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; |
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// gather all of the information from the Bass file |
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|
100 |
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// get the stamps and globals; |
72 |
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the_stamps = stamps; |
73 |
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the_globals = globals; |
100 |
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gatherInfo(); |
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|
|
102 |
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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(); |
102 |
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// creation of complex system objects |
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|
|
104 |
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// get the ones we know are there, yet still may need some work. |
81 |
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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 ); |
104 |
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sysObjectsCreation(); |
105 |
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|
106 |
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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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|
106 |
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// initialize the system coordinates |
107 |
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|
108 |
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if ( !initSuspend ){ |
109 |
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initSystemCoords(); |
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|
111 |
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if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
112 |
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else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
113 |
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else{ |
94 |
< |
sprintf( painCave.errMsg, |
95 |
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"SimSetup Error. Unrecognized force field -> %s\n", |
96 |
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force_field ); |
97 |
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painCave.isFatal = 1; |
98 |
< |
simError(); |
99 |
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} |
111 |
> |
if( !(globals->getUseInitTime()) ) |
112 |
> |
info[0].currentTime = 0.0; |
113 |
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} |
114 |
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|
115 |
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#ifdef IS_MPI |
102 |
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strcpy( checkPointMsg, "ForceField creation successful" ); |
103 |
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MPIcheckPoint(); |
104 |
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#endif // is_mpi |
115 |
> |
// check on the post processing info |
116 |
|
|
117 |
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|
117 |
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finalInfoCheck(); |
118 |
|
|
119 |
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// get the components and calculate the tot_nMol and indvidual n_mol |
109 |
< |
the_components = the_globals->getComponents(); |
110 |
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components_nmol = new int[n_components]; |
111 |
< |
comp_stamps = new MoleculeStamp*[n_components]; |
119 |
> |
// make the output filenames |
120 |
|
|
121 |
< |
if( !the_globals->haveNMol() ){ |
114 |
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// we don't have the total number of molecules, so we assume it is |
115 |
< |
// given in each component |
121 |
> |
makeOutNames(); |
122 |
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|
123 |
< |
tot_nmol = 0; |
118 |
< |
for( i=0; i<n_components; i++ ){ |
123 |
> |
// make the integrator |
124 |
|
|
125 |
< |
if( !the_components[i]->haveNMol() ){ |
121 |
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// we have a problem |
122 |
< |
sprintf( painCave.errMsg, |
123 |
< |
"SimSetup Error. No global NMol or component NMol" |
124 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
125 |
< |
painCave.isFatal = 1; |
126 |
< |
simError(); |
127 |
< |
} |
125 |
> |
makeIntegrator(); |
126 |
|
|
129 |
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tot_nmol += the_components[i]->getNMol(); |
130 |
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components_nmol[i] = the_components[i]->getNMol(); |
131 |
– |
} |
132 |
– |
} |
133 |
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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 |
– |
" Please give nMol in the components.\n" ); |
140 |
– |
painCave.isFatal = 1; |
141 |
– |
simError(); |
142 |
– |
|
143 |
– |
|
144 |
– |
// tot_nmol = the_globals->getNMol(); |
145 |
– |
|
146 |
– |
// //we have the total number of molecules, now we check for molfractions |
147 |
– |
// for( i=0; i<n_components; i++ ){ |
148 |
– |
|
149 |
– |
// if( !the_components[i]->haveMolFraction() ){ |
150 |
– |
|
151 |
– |
// if( !the_components[i]->haveNMol() ){ |
152 |
– |
// //we have a problem |
153 |
– |
// std::cerr << "SimSetup error. Neither molFraction nor " |
154 |
– |
// << " nMol was given in component |
155 |
– |
|
156 |
– |
} |
157 |
– |
|
127 |
|
#ifdef IS_MPI |
128 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
129 |
< |
MPIcheckPoint(); |
161 |
< |
#endif // is_mpi |
128 |
> |
mpiSim->mpiRefresh(); |
129 |
> |
#endif |
130 |
|
|
131 |
< |
// make an array of molecule stamps that match the components used. |
164 |
< |
// also extract the used stamps out into a separate linked list |
131 |
> |
// initialize the Fortran |
132 |
|
|
133 |
< |
simnfo->nComponents = n_components; |
134 |
< |
simnfo->componentsNmol = components_nmol; |
168 |
< |
simnfo->compStamps = comp_stamps; |
169 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
170 |
< |
|
171 |
< |
char* id; |
172 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
173 |
< |
LinkedMolStamp* currentStamp = NULL; |
174 |
< |
for( i=0; i<n_components; i++ ){ |
133 |
> |
initFortran(); |
134 |
> |
} |
135 |
|
|
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 |
136 |
|
|
137 |
< |
comp_stamps[i] = headStamp->match( id ); |
138 |
< |
if( comp_stamps[i] == NULL ){ |
139 |
< |
|
140 |
< |
// extract the component from the list; |
141 |
< |
|
142 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
143 |
< |
if( currentStamp == NULL ){ |
144 |
< |
sprintf( painCave.errMsg, |
145 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
146 |
< |
"list of declared molecules\n", |
147 |
< |
id ); |
192 |
< |
painCave.isFatal = 1; |
193 |
< |
simError(); |
194 |
< |
} |
195 |
< |
|
196 |
< |
headStamp->add( currentStamp ); |
197 |
< |
comp_stamps[i] = headStamp->match( id ); |
198 |
< |
} |
199 |
< |
} |
137 |
> |
void SimSetup::makeMolecules(void){ |
138 |
> |
int k; |
139 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
140 |
> |
molInit molInfo; |
141 |
> |
DirectionalAtom* dAtom; |
142 |
> |
LinkedAssign* extras; |
143 |
> |
LinkedAssign* current_extra; |
144 |
> |
AtomStamp* currentAtom; |
145 |
> |
BondStamp* currentBond; |
146 |
> |
BendStamp* currentBend; |
147 |
> |
TorsionStamp* currentTorsion; |
148 |
|
|
149 |
< |
#ifdef IS_MPI |
150 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
151 |
< |
MPIcheckPoint(); |
204 |
< |
#endif // is_mpi |
205 |
< |
|
149 |
> |
bond_pair* theBonds; |
150 |
> |
bend_set* theBends; |
151 |
> |
torsion_set* theTorsions; |
152 |
|
|
153 |
|
|
154 |
+ |
//init the forceField paramters |
155 |
|
|
156 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
156 |
> |
the_ff->readParams(); |
157 |
|
|
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 |
– |
} |
158 |
|
|
159 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
159 |
> |
// init the atoms |
160 |
|
|
161 |
< |
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; |
161 |
> |
double ux, uy, uz, u, uSqr; |
162 |
|
|
163 |
< |
|
164 |
< |
#ifdef IS_MPI |
163 |
> |
for (k = 0; k < nInfo; k++){ |
164 |
> |
the_ff->setSimInfo(&(info[k])); |
165 |
|
|
166 |
< |
// divide the molecules among processors here. |
167 |
< |
|
168 |
< |
mpiSim = new mpiSimulation( simnfo ); |
169 |
< |
|
239 |
< |
|
166 |
> |
atomOffset = 0; |
167 |
> |
excludeOffset = 0; |
168 |
> |
for (i = 0; i < info[k].n_mol; i++){ |
169 |
> |
stampID = info[k].molecules[i].getStampID(); |
170 |
|
|
171 |
< |
globalIndex = mpiSim->divideLabor(); |
171 |
> |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
172 |
> |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
173 |
> |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
174 |
> |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
175 |
> |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
176 |
|
|
177 |
+ |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
178 |
+ |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
179 |
+ |
molInfo.myBonds = new Bond * [molInfo.nBonds]; |
180 |
+ |
molInfo.myBends = new Bend * [molInfo.nBends]; |
181 |
+ |
molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
182 |
|
|
183 |
+ |
theBonds = new bond_pair[molInfo.nBonds]; |
184 |
+ |
theBends = new bend_set[molInfo.nBends]; |
185 |
+ |
theTorsions = new torsion_set[molInfo.nTorsions]; |
186 |
|
|
187 |
< |
// set up the local variables |
246 |
< |
|
247 |
< |
int localMol, allMol; |
248 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
187 |
> |
// make the Atoms |
188 |
|
|
189 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
190 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
191 |
< |
|
192 |
< |
allMol = 0; |
193 |
< |
localMol = 0; |
194 |
< |
local_atoms = 0; |
195 |
< |
local_bonds = 0; |
257 |
< |
local_bends = 0; |
258 |
< |
local_torsions = 0; |
259 |
< |
for( i=0; i<n_components; i++ ){ |
189 |
> |
for (j = 0; j < molInfo.nAtoms; j++){ |
190 |
> |
currentAtom = comp_stamps[stampID]->getAtom(j); |
191 |
> |
if (currentAtom->haveOrientation()){ |
192 |
> |
dAtom = new DirectionalAtom((j + atomOffset), |
193 |
> |
info[k].getConfiguration()); |
194 |
> |
info[k].n_oriented++; |
195 |
> |
molInfo.myAtoms[j] = dAtom; |
196 |
|
|
197 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
198 |
< |
|
199 |
< |
if( mol2proc[j] == worldRank ){ |
264 |
< |
|
265 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
266 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
267 |
< |
local_bends += comp_stamps[i]->getNBends(); |
268 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
269 |
< |
localMol++; |
270 |
< |
} |
271 |
< |
allMol++; |
272 |
< |
} |
273 |
< |
} |
274 |
< |
local_SRI = local_bonds + local_bends + local_torsions; |
275 |
< |
|
197 |
> |
ux = currentAtom->getOrntX(); |
198 |
> |
uy = currentAtom->getOrntY(); |
199 |
> |
uz = currentAtom->getOrntZ(); |
200 |
|
|
201 |
< |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
278 |
< |
|
279 |
< |
if( local_atoms != simnfo->n_atoms ){ |
280 |
< |
sprintf( painCave.errMsg, |
281 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
282 |
< |
" localAtom (%d) are not equal.\n", |
283 |
< |
simnfo->n_atoms, |
284 |
< |
local_atoms ); |
285 |
< |
painCave.isFatal = 1; |
286 |
< |
simError(); |
287 |
< |
} |
201 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
202 |
|
|
203 |
< |
simnfo->n_bonds = local_bonds; |
204 |
< |
simnfo->n_bends = local_bends; |
205 |
< |
simnfo->n_torsions = local_torsions; |
206 |
< |
simnfo->n_SRI = local_SRI; |
293 |
< |
simnfo->n_mol = localMol; |
203 |
> |
u = sqrt(uSqr); |
204 |
> |
ux = ux / u; |
205 |
> |
uy = uy / u; |
206 |
> |
uz = uz / u; |
207 |
|
|
208 |
< |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
209 |
< |
MPIcheckPoint(); |
210 |
< |
|
211 |
< |
|
212 |
< |
#endif // is_mpi |
213 |
< |
|
208 |
> |
dAtom->setSUx(ux); |
209 |
> |
dAtom->setSUy(uy); |
210 |
> |
dAtom->setSUz(uz); |
211 |
> |
} |
212 |
> |
else{ |
213 |
> |
molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
214 |
> |
info[k].getConfiguration()); |
215 |
> |
} |
216 |
> |
molInfo.myAtoms[j]->setType(currentAtom->getType()); |
217 |
|
|
218 |
< |
// create the atom and short range interaction arrays |
218 |
> |
#ifdef IS_MPI |
219 |
|
|
220 |
< |
Atom::createArrays(simnfo->n_atoms); |
305 |
< |
the_atoms = new Atom*[simnfo->n_atoms]; |
306 |
< |
the_molecules = new Molecule[simnfo->n_mol]; |
307 |
< |
int molIndex; |
220 |
> |
molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
221 |
|
|
222 |
< |
// initialize the molecule's stampID's |
222 |
> |
#endif // is_mpi |
223 |
> |
} |
224 |
|
|
225 |
+ |
// make the bonds |
226 |
+ |
for (j = 0; j < molInfo.nBonds; j++){ |
227 |
+ |
currentBond = comp_stamps[stampID]->getBond(j); |
228 |
+ |
theBonds[j].a = currentBond->getA() + atomOffset; |
229 |
+ |
theBonds[j].b = currentBond->getB() + atomOffset; |
230 |
+ |
|
231 |
+ |
exI = theBonds[j].a; |
232 |
+ |
exJ = theBonds[j].b; |
233 |
+ |
|
234 |
+ |
// exclude_I must always be the smaller of the pair |
235 |
+ |
if (exI > exJ){ |
236 |
+ |
tempEx = exI; |
237 |
+ |
exI = exJ; |
238 |
+ |
exJ = tempEx; |
239 |
+ |
} |
240 |
|
#ifdef IS_MPI |
241 |
< |
|
241 |
> |
tempEx = exI; |
242 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
243 |
> |
tempEx = exJ; |
244 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
245 |
|
|
246 |
< |
molIndex = 0; |
247 |
< |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
316 |
< |
|
317 |
< |
if(mol2proc[i] == worldRank ){ |
318 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
319 |
< |
molIndex++; |
320 |
< |
} |
321 |
< |
} |
246 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
247 |
> |
#else // isn't MPI |
248 |
|
|
249 |
< |
#else // is_mpi |
250 |
< |
|
251 |
< |
molIndex = 0; |
252 |
< |
for(i=0; i<n_components; i++){ |
327 |
< |
for(j=0; j<components_nmol[i]; j++ ){ |
328 |
< |
the_molecules[molIndex].setStampID( i ); |
329 |
< |
molIndex++; |
330 |
< |
} |
331 |
< |
} |
332 |
< |
|
249 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
250 |
> |
#endif //is_mpi |
251 |
> |
} |
252 |
> |
excludeOffset += molInfo.nBonds; |
253 |
|
|
254 |
< |
#endif // is_mpi |
254 |
> |
//make the bends |
255 |
> |
for (j = 0; j < molInfo.nBends; j++){ |
256 |
> |
currentBend = comp_stamps[stampID]->getBend(j); |
257 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
258 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
259 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
260 |
|
|
261 |
+ |
if (currentBend->haveExtras()){ |
262 |
+ |
extras = currentBend->getExtras(); |
263 |
+ |
current_extra = extras; |
264 |
|
|
265 |
< |
if( simnfo->n_SRI ){ |
266 |
< |
Exclude::createArray(simnfo->n_SRI); |
267 |
< |
the_excludes = new Exclude*[simnfo->n_SRI]; |
268 |
< |
simnfo->globalExcludes = new int; |
269 |
< |
simnfo->n_exclude = tot_SRI; |
270 |
< |
} |
271 |
< |
else{ |
344 |
< |
|
345 |
< |
Exclude::createArray( 1 ); |
346 |
< |
the_excludes = new Exclude*; |
347 |
< |
the_excludes[0] = new Exclude(0); |
348 |
< |
the_excludes[0]->setPair( 0,0 ); |
349 |
< |
simnfo->globalExcludes = new int; |
350 |
< |
simnfo->globalExcludes[0] = 0; |
351 |
< |
simnfo->n_exclude = 0; |
352 |
< |
} |
265 |
> |
while (current_extra != NULL){ |
266 |
> |
if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
267 |
> |
switch (current_extra->getType()){ |
268 |
> |
case 0: |
269 |
> |
theBends[j].ghost = current_extra->getInt() + atomOffset; |
270 |
> |
theBends[j].isGhost = 1; |
271 |
> |
break; |
272 |
|
|
273 |
< |
// set the arrays into the SimInfo object |
273 |
> |
case 1: |
274 |
> |
theBends[j].ghost = (int) current_extra->getDouble() + |
275 |
> |
atomOffset; |
276 |
> |
theBends[j].isGhost = 1; |
277 |
> |
break; |
278 |
|
|
279 |
< |
simnfo->atoms = the_atoms; |
280 |
< |
simnfo->molecules = the_molecules; |
281 |
< |
simnfo->nGlobalExcludes = 0; |
282 |
< |
simnfo->excludes = the_excludes; |
279 |
> |
default: |
280 |
> |
sprintf(painCave.errMsg, |
281 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
282 |
> |
"double nor an int.\n" |
283 |
> |
"-->Bend[%d] in %s\n", |
284 |
> |
j, comp_stamps[stampID]->getID()); |
285 |
> |
painCave.isFatal = 1; |
286 |
> |
simError(); |
287 |
> |
} |
288 |
> |
} |
289 |
> |
else{ |
290 |
> |
sprintf(painCave.errMsg, |
291 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
292 |
> |
" -->%s in Bend[%d] in %s\n", |
293 |
> |
current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
294 |
> |
painCave.isFatal = 1; |
295 |
> |
simError(); |
296 |
> |
} |
297 |
|
|
298 |
+ |
current_extra = current_extra->getNext(); |
299 |
+ |
} |
300 |
+ |
} |
301 |
|
|
302 |
< |
// get some of the tricky things that may still be in the globals |
302 |
> |
if (!theBends[j].isGhost){ |
303 |
> |
exI = theBends[j].a; |
304 |
> |
exJ = theBends[j].c; |
305 |
> |
} |
306 |
> |
else{ |
307 |
> |
exI = theBends[j].a; |
308 |
> |
exJ = theBends[j].b; |
309 |
> |
} |
310 |
|
|
311 |
< |
|
312 |
< |
if( the_globals->haveBox() ){ |
313 |
< |
simnfo->box_x = the_globals->getBox(); |
314 |
< |
simnfo->box_y = the_globals->getBox(); |
315 |
< |
simnfo->box_z = the_globals->getBox(); |
316 |
< |
} |
317 |
< |
else if( the_globals->haveDensity() ){ |
311 |
> |
// exclude_I must always be the smaller of the pair |
312 |
> |
if (exI > exJ){ |
313 |
> |
tempEx = exI; |
314 |
> |
exI = exJ; |
315 |
> |
exJ = tempEx; |
316 |
> |
} |
317 |
> |
#ifdef IS_MPI |
318 |
> |
tempEx = exI; |
319 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
320 |
> |
tempEx = exJ; |
321 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
322 |
|
|
323 |
< |
double vol; |
324 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
325 |
< |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
326 |
< |
simnfo->box_y = simnfo->box_x; |
327 |
< |
simnfo->box_z = simnfo->box_x; |
328 |
< |
} |
378 |
< |
else{ |
379 |
< |
if( !the_globals->haveBoxX() ){ |
380 |
< |
sprintf( painCave.errMsg, |
381 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
382 |
< |
painCave.isFatal = 1; |
383 |
< |
simError(); |
384 |
< |
} |
385 |
< |
simnfo->box_x = the_globals->getBoxX(); |
323 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
324 |
> |
#else // isn't MPI |
325 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
326 |
> |
#endif //is_mpi |
327 |
> |
} |
328 |
> |
excludeOffset += molInfo.nBends; |
329 |
|
|
330 |
< |
if( !the_globals->haveBoxY() ){ |
331 |
< |
sprintf( painCave.errMsg, |
332 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
333 |
< |
painCave.isFatal = 1; |
334 |
< |
simError(); |
335 |
< |
} |
393 |
< |
simnfo->box_y = the_globals->getBoxY(); |
330 |
> |
for (j = 0; j < molInfo.nTorsions; j++){ |
331 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion(j); |
332 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
333 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
334 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
335 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
336 |
|
|
337 |
< |
if( !the_globals->haveBoxZ() ){ |
338 |
< |
sprintf( painCave.errMsg, |
339 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
340 |
< |
painCave.isFatal = 1; |
341 |
< |
simError(); |
337 |
> |
exI = theTorsions[j].a; |
338 |
> |
exJ = theTorsions[j].d; |
339 |
> |
|
340 |
> |
// exclude_I must always be the smaller of the pair |
341 |
> |
if (exI > exJ){ |
342 |
> |
tempEx = exI; |
343 |
> |
exI = exJ; |
344 |
> |
exJ = tempEx; |
345 |
> |
} |
346 |
> |
#ifdef IS_MPI |
347 |
> |
tempEx = exI; |
348 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
349 |
> |
tempEx = exJ; |
350 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
351 |
> |
|
352 |
> |
info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
353 |
> |
#else // isn't MPI |
354 |
> |
info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
355 |
> |
#endif //is_mpi |
356 |
> |
} |
357 |
> |
excludeOffset += molInfo.nTorsions; |
358 |
> |
|
359 |
> |
|
360 |
> |
// send the arrays off to the forceField for init. |
361 |
> |
|
362 |
> |
the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
363 |
> |
the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
364 |
> |
the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
365 |
> |
the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
366 |
> |
theTorsions); |
367 |
> |
|
368 |
> |
|
369 |
> |
info[k].molecules[i].initialize(molInfo); |
370 |
> |
|
371 |
> |
|
372 |
> |
atomOffset += molInfo.nAtoms; |
373 |
> |
delete[] theBonds; |
374 |
> |
delete[] theBends; |
375 |
> |
delete[] theTorsions; |
376 |
|
} |
401 |
– |
simnfo->box_z = the_globals->getBoxZ(); |
377 |
|
} |
378 |
|
|
379 |
|
#ifdef IS_MPI |
380 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
380 |
> |
sprintf(checkPointMsg, "all molecules initialized succesfully"); |
381 |
|
MPIcheckPoint(); |
382 |
|
#endif // is_mpi |
383 |
|
|
384 |
+ |
// clean up the forcefield |
385 |
|
|
386 |
< |
// initialize the arrays |
386 |
> |
the_ff->calcRcut(); |
387 |
> |
the_ff->cleanMe(); |
388 |
> |
} |
389 |
|
|
390 |
< |
the_ff->setSimInfo( simnfo ); |
390 |
> |
void SimSetup::initFromBass(void){ |
391 |
> |
int i, j, k; |
392 |
> |
int n_cells; |
393 |
> |
double cellx, celly, cellz; |
394 |
> |
double temp1, temp2, temp3; |
395 |
> |
int n_per_extra; |
396 |
> |
int n_extra; |
397 |
> |
int have_extra, done; |
398 |
|
|
399 |
< |
makeMolecules(); |
400 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
401 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
402 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
418 |
< |
} |
419 |
< |
|
420 |
< |
if (the_globals->getUseRF() ) { |
421 |
< |
simnfo->useReactionField = 1; |
422 |
< |
|
423 |
< |
if( !the_globals->haveECR() ){ |
424 |
< |
sprintf( painCave.errMsg, |
425 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
426 |
< |
"box length for the electrostaticCutoffRadius.\n" |
427 |
< |
"I hope you have a very fast processor!\n"); |
428 |
< |
painCave.isFatal = 0; |
429 |
< |
simError(); |
430 |
< |
double smallest; |
431 |
< |
smallest = simnfo->box_x; |
432 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
433 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
434 |
< |
simnfo->ecr = 0.5 * smallest; |
435 |
< |
} else { |
436 |
< |
simnfo->ecr = the_globals->getECR(); |
437 |
< |
} |
399 |
> |
double vel[3]; |
400 |
> |
vel[0] = 0.0; |
401 |
> |
vel[1] = 0.0; |
402 |
> |
vel[2] = 0.0; |
403 |
|
|
404 |
< |
if( !the_globals->haveEST() ){ |
405 |
< |
sprintf( painCave.errMsg, |
406 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
407 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
408 |
< |
); |
409 |
< |
painCave.isFatal = 0; |
410 |
< |
simError(); |
411 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
412 |
< |
} else { |
413 |
< |
simnfo->est = the_globals->getEST(); |
414 |
< |
} |
415 |
< |
|
416 |
< |
if(!the_globals->haveDielectric() ){ |
417 |
< |
sprintf( painCave.errMsg, |
418 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
419 |
< |
"setting a dielectric constant!\n" |
420 |
< |
); |
404 |
> |
temp1 = (double) tot_nmol / 4.0; |
405 |
> |
temp2 = pow(temp1, (1.0 / 3.0)); |
406 |
> |
temp3 = ceil(temp2); |
407 |
> |
|
408 |
> |
have_extra = 0; |
409 |
> |
if (temp2 < temp3){ |
410 |
> |
// we have a non-complete lattice |
411 |
> |
have_extra = 1; |
412 |
> |
|
413 |
> |
n_cells = (int) temp3 - 1; |
414 |
> |
cellx = info[0].boxL[0] / temp3; |
415 |
> |
celly = info[0].boxL[1] / temp3; |
416 |
> |
cellz = info[0].boxL[2] / temp3; |
417 |
> |
n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
418 |
> |
temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
419 |
> |
n_per_extra = (int) ceil(temp1); |
420 |
> |
|
421 |
> |
if (n_per_extra > 4){ |
422 |
> |
sprintf(painCave.errMsg, |
423 |
> |
"SimSetup error. There has been an error in constructing" |
424 |
> |
" the non-complete lattice.\n"); |
425 |
|
painCave.isFatal = 1; |
426 |
|
simError(); |
427 |
|
} |
428 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
429 |
< |
} else { |
430 |
< |
if (simnfo->n_dipoles) { |
431 |
< |
|
432 |
< |
if( !the_globals->haveECR() ){ |
433 |
< |
sprintf( painCave.errMsg, |
434 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
435 |
< |
"box length for the electrostaticCutoffRadius.\n" |
436 |
< |
"I hope you have a very fast processor!\n"); |
437 |
< |
painCave.isFatal = 0; |
438 |
< |
simError(); |
439 |
< |
double smallest; |
440 |
< |
smallest = simnfo->box_x; |
441 |
< |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
442 |
< |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
443 |
< |
simnfo->ecr = 0.5 * smallest; |
444 |
< |
} else { |
445 |
< |
simnfo->ecr = the_globals->getECR(); |
428 |
> |
} |
429 |
> |
else{ |
430 |
> |
n_cells = (int) temp3; |
431 |
> |
cellx = info[0].boxL[0] / temp3; |
432 |
> |
celly = info[0].boxL[1] / temp3; |
433 |
> |
cellz = info[0].boxL[2] / temp3; |
434 |
> |
} |
435 |
> |
|
436 |
> |
current_mol = 0; |
437 |
> |
current_comp_mol = 0; |
438 |
> |
current_comp = 0; |
439 |
> |
current_atom_ndx = 0; |
440 |
> |
|
441 |
> |
for (i = 0; i < n_cells ; i++){ |
442 |
> |
for (j = 0; j < n_cells; j++){ |
443 |
> |
for (k = 0; k < n_cells; k++){ |
444 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
445 |
> |
|
446 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
447 |
> |
|
448 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
449 |
> |
|
450 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
451 |
|
} |
478 |
– |
|
479 |
– |
if( !the_globals->haveEST() ){ |
480 |
– |
sprintf( painCave.errMsg, |
481 |
– |
"SimSetup Warning: using default value of 5% of the" |
482 |
– |
"electrostaticCutoffRadius for the " |
483 |
– |
"electrostaticSkinThickness\n" |
484 |
– |
); |
485 |
– |
painCave.isFatal = 0; |
486 |
– |
simError(); |
487 |
– |
simnfo->est = 0.05 * simnfo->ecr; |
488 |
– |
} else { |
489 |
– |
simnfo->est = the_globals->getEST(); |
490 |
– |
} |
452 |
|
} |
453 |
< |
} |
453 |
> |
} |
454 |
|
|
455 |
< |
#ifdef IS_MPI |
456 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
496 |
< |
MPIcheckPoint(); |
497 |
< |
#endif // is_mpi |
455 |
> |
if (have_extra){ |
456 |
> |
done = 0; |
457 |
|
|
458 |
< |
if( the_globals->haveInitialConfig() ){ |
459 |
< |
|
460 |
< |
InitializeFromFile* fileInit; |
461 |
< |
#ifdef IS_MPI // is_mpi |
462 |
< |
if( worldRank == 0 ){ |
463 |
< |
#endif //is_mpi |
464 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
465 |
< |
#ifdef IS_MPI |
466 |
< |
}else fileInit = new InitializeFromFile( NULL ); |
467 |
< |
#endif |
468 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
458 |
> |
int start_ndx; |
459 |
> |
for (i = 0; i < (n_cells + 1) && !done; i++){ |
460 |
> |
for (j = 0; j < (n_cells + 1) && !done; j++){ |
461 |
> |
if (i < n_cells){ |
462 |
> |
if (j < n_cells){ |
463 |
> |
start_ndx = n_cells; |
464 |
> |
} |
465 |
> |
else |
466 |
> |
start_ndx = 0; |
467 |
> |
} |
468 |
> |
else |
469 |
> |
start_ndx = 0; |
470 |
|
|
471 |
< |
delete fileInit; |
472 |
< |
} |
473 |
< |
else{ |
471 |
> |
for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
472 |
> |
makeElement(i * cellx, j * celly, k * cellz); |
473 |
> |
done = (current_mol >= tot_nmol); |
474 |
|
|
475 |
< |
#ifdef IS_MPI |
475 |
> |
if (!done && n_per_extra > 1){ |
476 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
477 |
> |
k * cellz); |
478 |
> |
done = (current_mol >= tot_nmol); |
479 |
> |
} |
480 |
|
|
481 |
< |
// no init from bass |
482 |
< |
|
483 |
< |
sprintf( painCave.errMsg, |
484 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
485 |
< |
painCave.isFatal; |
522 |
< |
simError(); |
523 |
< |
|
524 |
< |
#else |
481 |
> |
if (!done && n_per_extra > 2){ |
482 |
> |
makeElement(i * cellx, j * celly + 0.5 * celly, |
483 |
> |
k * cellz + 0.5 * cellz); |
484 |
> |
done = (current_mol >= tot_nmol); |
485 |
> |
} |
486 |
|
|
487 |
< |
initFromBass(); |
487 |
> |
if (!done && n_per_extra > 3){ |
488 |
> |
makeElement(i * cellx + 0.5 * cellx, j * celly, |
489 |
> |
k * cellz + 0.5 * cellz); |
490 |
> |
done = (current_mol >= tot_nmol); |
491 |
> |
} |
492 |
> |
} |
493 |
> |
} |
494 |
> |
} |
495 |
> |
} |
496 |
|
|
497 |
+ |
for (i = 0; i < info[0].n_atoms; i++){ |
498 |
+ |
info[0].atoms[i]->setVel(vel); |
499 |
+ |
} |
500 |
+ |
} |
501 |
|
|
502 |
< |
#endif |
503 |
< |
} |
502 |
> |
void SimSetup::makeElement(double x, double y, double z){ |
503 |
> |
int k; |
504 |
> |
AtomStamp* current_atom; |
505 |
> |
DirectionalAtom* dAtom; |
506 |
> |
double rotMat[3][3]; |
507 |
> |
double pos[3]; |
508 |
|
|
509 |
< |
#ifdef IS_MPI |
510 |
< |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
511 |
< |
MPIcheckPoint(); |
512 |
< |
#endif // is_mpi |
509 |
> |
for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
510 |
> |
current_atom = comp_stamps[current_comp]->getAtom(k); |
511 |
> |
if (!current_atom->havePosition()){ |
512 |
> |
sprintf(painCave.errMsg, |
513 |
> |
"SimSetup:initFromBass error.\n" |
514 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
515 |
> |
"\tThe initialization routine is unable to give a start" |
516 |
> |
" position.\n", |
517 |
> |
comp_stamps[current_comp]->getID(), current_atom->getType()); |
518 |
> |
painCave.isFatal = 1; |
519 |
> |
simError(); |
520 |
> |
} |
521 |
|
|
522 |
+ |
pos[0] = x + current_atom->getPosX(); |
523 |
+ |
pos[1] = y + current_atom->getPosY(); |
524 |
+ |
pos[2] = z + current_atom->getPosZ(); |
525 |
|
|
526 |
< |
|
539 |
< |
|
540 |
< |
|
526 |
> |
info[0].atoms[current_atom_ndx]->setPos(pos); |
527 |
|
|
528 |
< |
|
529 |
< |
#ifdef IS_MPI |
530 |
< |
if( worldRank == 0 ){ |
531 |
< |
#endif // is_mpi |
532 |
< |
|
533 |
< |
if( the_globals->haveFinalConfig() ){ |
534 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
528 |
> |
if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
529 |
> |
dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
530 |
> |
|
531 |
> |
rotMat[0][0] = 1.0; |
532 |
> |
rotMat[0][1] = 0.0; |
533 |
> |
rotMat[0][2] = 0.0; |
534 |
> |
|
535 |
> |
rotMat[1][0] = 0.0; |
536 |
> |
rotMat[1][1] = 1.0; |
537 |
> |
rotMat[1][2] = 0.0; |
538 |
> |
|
539 |
> |
rotMat[2][0] = 0.0; |
540 |
> |
rotMat[2][1] = 0.0; |
541 |
> |
rotMat[2][2] = 1.0; |
542 |
> |
|
543 |
> |
dAtom->setA(rotMat); |
544 |
|
} |
550 |
– |
else{ |
551 |
– |
strcpy( simnfo->finalName, inFileName ); |
552 |
– |
char* endTest; |
553 |
– |
int nameLength = strlen( simnfo->finalName ); |
554 |
– |
endTest = &(simnfo->finalName[nameLength - 5]); |
555 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
556 |
– |
strcpy( endTest, ".eor" ); |
557 |
– |
} |
558 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
559 |
– |
strcpy( endTest, ".eor" ); |
560 |
– |
} |
561 |
– |
else{ |
562 |
– |
endTest = &(simnfo->finalName[nameLength - 4]); |
563 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
564 |
– |
strcpy( endTest, ".eor" ); |
565 |
– |
} |
566 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
567 |
– |
strcpy( endTest, ".eor" ); |
568 |
– |
} |
569 |
– |
else{ |
570 |
– |
strcat( simnfo->finalName, ".eor" ); |
571 |
– |
} |
572 |
– |
} |
573 |
– |
} |
574 |
– |
|
575 |
– |
// make the sample and status out names |
576 |
– |
|
577 |
– |
strcpy( simnfo->sampleName, inFileName ); |
578 |
– |
char* endTest; |
579 |
– |
int nameLength = strlen( simnfo->sampleName ); |
580 |
– |
endTest = &(simnfo->sampleName[nameLength - 5]); |
581 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
582 |
– |
strcpy( endTest, ".dump" ); |
583 |
– |
} |
584 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
585 |
– |
strcpy( endTest, ".dump" ); |
586 |
– |
} |
587 |
– |
else{ |
588 |
– |
endTest = &(simnfo->sampleName[nameLength - 4]); |
589 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
590 |
– |
strcpy( endTest, ".dump" ); |
591 |
– |
} |
592 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
593 |
– |
strcpy( endTest, ".dump" ); |
594 |
– |
} |
595 |
– |
else{ |
596 |
– |
strcat( simnfo->sampleName, ".dump" ); |
597 |
– |
} |
598 |
– |
} |
599 |
– |
|
600 |
– |
strcpy( simnfo->statusName, inFileName ); |
601 |
– |
nameLength = strlen( simnfo->statusName ); |
602 |
– |
endTest = &(simnfo->statusName[nameLength - 5]); |
603 |
– |
if( !strcmp( endTest, ".bass" ) ){ |
604 |
– |
strcpy( endTest, ".stat" ); |
605 |
– |
} |
606 |
– |
else if( !strcmp( endTest, ".BASS" ) ){ |
607 |
– |
strcpy( endTest, ".stat" ); |
608 |
– |
} |
609 |
– |
else{ |
610 |
– |
endTest = &(simnfo->statusName[nameLength - 4]); |
611 |
– |
if( !strcmp( endTest, ".bss" ) ){ |
612 |
– |
strcpy( endTest, ".stat" ); |
613 |
– |
} |
614 |
– |
else if( !strcmp( endTest, ".mdl" ) ){ |
615 |
– |
strcpy( endTest, ".stat" ); |
616 |
– |
} |
617 |
– |
else{ |
618 |
– |
strcat( simnfo->statusName, ".stat" ); |
619 |
– |
} |
620 |
– |
} |
621 |
– |
|
622 |
– |
#ifdef IS_MPI |
623 |
– |
} |
624 |
– |
#endif // is_mpi |
625 |
– |
|
626 |
– |
// set the status, sample, and themal kick times |
627 |
– |
|
628 |
– |
if( the_globals->haveSampleTime() ){ |
629 |
– |
simnfo->sampleTime = the_globals->getSampleTime(); |
630 |
– |
simnfo->statusTime = simnfo->sampleTime; |
631 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
632 |
– |
} |
633 |
– |
else{ |
634 |
– |
simnfo->sampleTime = the_globals->getRunTime(); |
635 |
– |
simnfo->statusTime = simnfo->sampleTime; |
636 |
– |
simnfo->thermalTime = simnfo->sampleTime; |
637 |
– |
} |
545 |
|
|
546 |
< |
if( the_globals->haveStatusTime() ){ |
640 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
546 |
> |
current_atom_ndx++; |
547 |
|
} |
548 |
|
|
549 |
< |
if( the_globals->haveThermalTime() ){ |
550 |
< |
simnfo->thermalTime = the_globals->getThermalTime(); |
549 |
> |
current_mol++; |
550 |
> |
current_comp_mol++; |
551 |
> |
|
552 |
> |
if (current_comp_mol >= components_nmol[current_comp]){ |
553 |
> |
current_comp_mol = 0; |
554 |
> |
current_comp++; |
555 |
|
} |
556 |
+ |
} |
557 |
|
|
647 |
– |
// check for the temperature set flag |
558 |
|
|
559 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
559 |
> |
void SimSetup::gatherInfo(void){ |
560 |
> |
int i; |
561 |
|
|
562 |
+ |
ensembleCase = -1; |
563 |
+ |
ffCase = -1; |
564 |
|
|
565 |
< |
// // make the longe range forces and the integrator |
565 |
> |
// set the easy ones first |
566 |
|
|
567 |
< |
// new AllLong( simnfo ); |
567 |
> |
for (i = 0; i < nInfo; i++){ |
568 |
> |
info[i].target_temp = globals->getTargetTemp(); |
569 |
> |
info[i].dt = globals->getDt(); |
570 |
> |
info[i].run_time = globals->getRunTime(); |
571 |
> |
} |
572 |
> |
n_components = globals->getNComponents(); |
573 |
|
|
656 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
657 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
574 |
|
|
575 |
+ |
// get the forceField |
576 |
|
|
577 |
+ |
strcpy(force_field, globals->getForceField()); |
578 |
|
|
579 |
< |
// initialize the Fortran |
580 |
< |
|
663 |
< |
simnfo->refreshSim(); |
664 |
< |
|
665 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
666 |
< |
the_ff->initForceField( LB_MIXING_RULE ); |
579 |
> |
if (!strcasecmp(force_field, "DUFF")){ |
580 |
> |
ffCase = FF_DUFF; |
581 |
|
} |
582 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
583 |
< |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
582 |
> |
else if (!strcasecmp(force_field, "LJ")){ |
583 |
> |
ffCase = FF_LJ; |
584 |
|
} |
585 |
+ |
else if (!strcasecmp(force_field, "EAM")){ |
586 |
+ |
ffCase = FF_EAM; |
587 |
+ |
} |
588 |
|
else{ |
589 |
< |
sprintf( painCave.errMsg, |
590 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
591 |
< |
simnfo->mixingRule ); |
592 |
< |
painCave.isFatal = 1; |
676 |
< |
simError(); |
589 |
> |
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
590 |
> |
force_field); |
591 |
> |
painCave.isFatal = 1; |
592 |
> |
simError(); |
593 |
|
} |
594 |
|
|
595 |
+ |
// get the ensemble |
596 |
|
|
597 |
< |
#ifdef IS_MPI |
681 |
< |
strcpy( checkPointMsg, |
682 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
683 |
< |
MPIcheckPoint(); |
684 |
< |
#endif // is_mpi |
685 |
< |
} |
686 |
< |
|
687 |
< |
|
688 |
< |
void SimSetup::makeMolecules( void ){ |
689 |
< |
|
690 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
691 |
< |
molInit info; |
692 |
< |
DirectionalAtom* dAtom; |
693 |
< |
LinkedAssign* extras; |
694 |
< |
LinkedAssign* current_extra; |
695 |
< |
AtomStamp* currentAtom; |
696 |
< |
BondStamp* currentBond; |
697 |
< |
BendStamp* currentBend; |
698 |
< |
TorsionStamp* currentTorsion; |
699 |
< |
|
700 |
< |
bond_pair* theBonds; |
701 |
< |
bend_set* theBends; |
702 |
< |
torsion_set* theTorsions; |
703 |
< |
|
704 |
< |
|
705 |
< |
//init the forceField paramters |
706 |
< |
|
707 |
< |
the_ff->readParams(); |
708 |
< |
|
709 |
< |
|
710 |
< |
// init the atoms |
711 |
< |
|
712 |
< |
double ux, uy, uz, u, uSqr; |
713 |
< |
|
714 |
< |
atomOffset = 0; |
715 |
< |
excludeOffset = 0; |
716 |
< |
for(i=0; i<simnfo->n_mol; i++){ |
717 |
< |
|
718 |
< |
stampID = the_molecules[i].getStampID(); |
719 |
< |
|
720 |
< |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
721 |
< |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
722 |
< |
info.nBends = comp_stamps[stampID]->getNBends(); |
723 |
< |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
724 |
< |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
725 |
< |
|
726 |
< |
info.myAtoms = &the_atoms[atomOffset]; |
727 |
< |
info.myExcludes = &the_excludes[excludeOffset]; |
728 |
< |
info.myBonds = new Bond*[info.nBonds]; |
729 |
< |
info.myBends = new Bend*[info.nBends]; |
730 |
< |
info.myTorsions = new Torsion*[info.nTorsions]; |
731 |
< |
|
732 |
< |
theBonds = new bond_pair[info.nBonds]; |
733 |
< |
theBends = new bend_set[info.nBends]; |
734 |
< |
theTorsions = new torsion_set[info.nTorsions]; |
735 |
< |
|
736 |
< |
// make the Atoms |
737 |
< |
|
738 |
< |
for(j=0; j<info.nAtoms; j++){ |
739 |
< |
|
740 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
741 |
< |
if( currentAtom->haveOrientation() ){ |
742 |
< |
|
743 |
< |
dAtom = new DirectionalAtom(j + atomOffset); |
744 |
< |
simnfo->n_oriented++; |
745 |
< |
info.myAtoms[j] = dAtom; |
746 |
< |
|
747 |
< |
ux = currentAtom->getOrntX(); |
748 |
< |
uy = currentAtom->getOrntY(); |
749 |
< |
uz = currentAtom->getOrntZ(); |
750 |
< |
|
751 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
752 |
< |
|
753 |
< |
u = sqrt( uSqr ); |
754 |
< |
ux = ux / u; |
755 |
< |
uy = uy / u; |
756 |
< |
uz = uz / u; |
757 |
< |
|
758 |
< |
dAtom->setSUx( ux ); |
759 |
< |
dAtom->setSUy( uy ); |
760 |
< |
dAtom->setSUz( uz ); |
761 |
< |
} |
762 |
< |
else{ |
763 |
< |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
764 |
< |
} |
765 |
< |
info.myAtoms[j]->setType( currentAtom->getType() ); |
766 |
< |
|
767 |
< |
#ifdef IS_MPI |
768 |
< |
|
769 |
< |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
770 |
< |
|
771 |
< |
#endif // is_mpi |
772 |
< |
} |
773 |
< |
|
774 |
< |
// make the bonds |
775 |
< |
for(j=0; j<info.nBonds; j++){ |
776 |
< |
|
777 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
778 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
779 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
597 |
> |
strcpy(ensemble, globals->getEnsemble()); |
598 |
|
|
599 |
< |
exI = theBonds[i].a; |
600 |
< |
exJ = theBonds[i].b; |
599 |
> |
if (!strcasecmp(ensemble, "NVE")){ |
600 |
> |
ensembleCase = NVE_ENS; |
601 |
> |
} |
602 |
> |
else if (!strcasecmp(ensemble, "NVT")){ |
603 |
> |
ensembleCase = NVT_ENS; |
604 |
> |
} |
605 |
> |
else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
606 |
> |
ensembleCase = NPTi_ENS; |
607 |
> |
} |
608 |
> |
else if (!strcasecmp(ensemble, "NPTf")){ |
609 |
> |
ensembleCase = NPTf_ENS; |
610 |
> |
} |
611 |
> |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
612 |
> |
ensembleCase = NPTxyz_ENS; |
613 |
> |
} |
614 |
> |
else{ |
615 |
> |
sprintf(painCave.errMsg, |
616 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
617 |
> |
"reverting to NVE for this simulation.\n", |
618 |
> |
ensemble); |
619 |
> |
painCave.isFatal = 0; |
620 |
> |
simError(); |
621 |
> |
strcpy(ensemble, "NVE"); |
622 |
> |
ensembleCase = NVE_ENS; |
623 |
> |
} |
624 |
|
|
625 |
< |
// exclude_I must always be the smaller of the pair |
626 |
< |
if( exI > exJ ){ |
786 |
< |
tempEx = exI; |
787 |
< |
exI = exJ; |
788 |
< |
exJ = tempEx; |
789 |
< |
} |
790 |
< |
#ifdef IS_MPI |
791 |
< |
tempEx = exI; |
792 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
793 |
< |
tempEx = exJ; |
794 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
795 |
< |
|
796 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
797 |
< |
#else // isn't MPI |
798 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
799 |
< |
#endif //is_mpi |
800 |
< |
} |
801 |
< |
excludeOffset += info.nBonds; |
625 |
> |
for (i = 0; i < nInfo; i++){ |
626 |
> |
strcpy(info[i].ensemble, ensemble); |
627 |
|
|
628 |
< |
//make the bends |
804 |
< |
for(j=0; j<info.nBends; j++){ |
805 |
< |
|
806 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
807 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
808 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
809 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
810 |
< |
|
811 |
< |
if( currentBend->haveExtras() ){ |
812 |
< |
|
813 |
< |
extras = currentBend->getExtras(); |
814 |
< |
current_extra = extras; |
815 |
< |
|
816 |
< |
while( current_extra != NULL ){ |
817 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
818 |
< |
|
819 |
< |
switch( current_extra->getType() ){ |
820 |
< |
|
821 |
< |
case 0: |
822 |
< |
theBends[j].ghost = |
823 |
< |
current_extra->getInt() + atomOffset; |
824 |
< |
theBends[j].isGhost = 1; |
825 |
< |
break; |
826 |
< |
|
827 |
< |
case 1: |
828 |
< |
theBends[j].ghost = |
829 |
< |
(int)current_extra->getDouble() + atomOffset; |
830 |
< |
theBends[j].isGhost = 1; |
831 |
< |
break; |
832 |
< |
|
833 |
< |
default: |
834 |
< |
sprintf( painCave.errMsg, |
835 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
836 |
< |
"double nor an int.\n" |
837 |
< |
"-->Bend[%d] in %s\n", |
838 |
< |
j, comp_stamps[stampID]->getID() ); |
839 |
< |
painCave.isFatal = 1; |
840 |
< |
simError(); |
841 |
< |
} |
842 |
< |
} |
843 |
< |
|
844 |
< |
else{ |
845 |
< |
|
846 |
< |
sprintf( painCave.errMsg, |
847 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
848 |
< |
" -->%s in Bend[%d] in %s\n", |
849 |
< |
current_extra->getlhs(), |
850 |
< |
j, comp_stamps[stampID]->getID() ); |
851 |
< |
painCave.isFatal = 1; |
852 |
< |
simError(); |
853 |
< |
} |
854 |
< |
|
855 |
< |
current_extra = current_extra->getNext(); |
856 |
< |
} |
857 |
< |
} |
858 |
< |
|
859 |
< |
if( !theBends[j].isGhost ){ |
860 |
< |
|
861 |
< |
exI = theBends[j].a; |
862 |
< |
exJ = theBends[j].c; |
863 |
< |
} |
864 |
< |
else{ |
865 |
< |
|
866 |
< |
exI = theBends[j].a; |
867 |
< |
exJ = theBends[j].b; |
868 |
< |
} |
869 |
< |
|
870 |
< |
// exclude_I must always be the smaller of the pair |
871 |
< |
if( exI > exJ ){ |
872 |
< |
tempEx = exI; |
873 |
< |
exI = exJ; |
874 |
< |
exJ = tempEx; |
875 |
< |
} |
876 |
< |
#ifdef IS_MPI |
877 |
< |
tempEx = exI; |
878 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
879 |
< |
tempEx = exJ; |
880 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
881 |
< |
|
882 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
883 |
< |
#else // isn't MPI |
884 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
885 |
< |
#endif //is_mpi |
886 |
< |
} |
887 |
< |
excludeOffset += info.nBends; |
628 |
> |
// get the mixing rule |
629 |
|
|
630 |
< |
for(j=0; j<info.nTorsions; j++){ |
631 |
< |
|
891 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
892 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
893 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
894 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
895 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
896 |
< |
|
897 |
< |
exI = theTorsions[j].a; |
898 |
< |
exJ = theTorsions[j].d; |
899 |
< |
|
900 |
< |
// exclude_I must always be the smaller of the pair |
901 |
< |
if( exI > exJ ){ |
902 |
< |
tempEx = exI; |
903 |
< |
exI = exJ; |
904 |
< |
exJ = tempEx; |
905 |
< |
} |
906 |
< |
#ifdef IS_MPI |
907 |
< |
tempEx = exI; |
908 |
< |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
909 |
< |
tempEx = exJ; |
910 |
< |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
911 |
< |
|
912 |
< |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
913 |
< |
#else // isn't MPI |
914 |
< |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
915 |
< |
#endif //is_mpi |
916 |
< |
} |
917 |
< |
excludeOffset += info.nTorsions; |
918 |
< |
|
919 |
< |
|
920 |
< |
// send the arrays off to the forceField for init. |
921 |
< |
|
922 |
< |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
923 |
< |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
924 |
< |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
925 |
< |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
926 |
< |
|
927 |
< |
|
928 |
< |
the_molecules[i].initialize( info ); |
929 |
< |
atomOffset += info.nAtoms; |
930 |
< |
delete[] theBonds; |
931 |
< |
delete[] theBends; |
932 |
< |
delete[] theTorsions; |
630 |
> |
strcpy(info[i].mixingRule, globals->getMixingRule()); |
631 |
> |
info[i].usePBC = globals->getPBC(); |
632 |
|
} |
633 |
|
|
634 |
< |
// clean up the forcefield |
936 |
< |
the_ff->calcRcut(); |
937 |
< |
the_ff->cleanMe(); |
938 |
< |
} |
634 |
> |
// get the components and calculate the tot_nMol and indvidual n_mol |
635 |
|
|
636 |
< |
void SimSetup::initFromBass( void ){ |
636 |
> |
the_components = globals->getComponents(); |
637 |
> |
components_nmol = new int[n_components]; |
638 |
|
|
942 |
– |
int i, j, k; |
943 |
– |
int n_cells; |
944 |
– |
double cellx, celly, cellz; |
945 |
– |
double temp1, temp2, temp3; |
946 |
– |
int n_per_extra; |
947 |
– |
int n_extra; |
948 |
– |
int have_extra, done; |
639 |
|
|
640 |
< |
temp1 = (double)tot_nmol / 4.0; |
641 |
< |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
642 |
< |
temp3 = ceil( temp2 ); |
640 |
> |
if (!globals->haveNMol()){ |
641 |
> |
// we don't have the total number of molecules, so we assume it is |
642 |
> |
// given in each component |
643 |
|
|
644 |
< |
have_extra =0; |
645 |
< |
if( temp2 < temp3 ){ // we have a non-complete lattice |
646 |
< |
have_extra =1; |
644 |
> |
tot_nmol = 0; |
645 |
> |
for (i = 0; i < n_components; i++){ |
646 |
> |
if (!the_components[i]->haveNMol()){ |
647 |
> |
// we have a problem |
648 |
> |
sprintf(painCave.errMsg, |
649 |
> |
"SimSetup Error. No global NMol or component NMol" |
650 |
> |
" given. Cannot calculate the number of atoms.\n"); |
651 |
> |
painCave.isFatal = 1; |
652 |
> |
simError(); |
653 |
> |
} |
654 |
|
|
655 |
< |
n_cells = (int)temp3 - 1; |
656 |
< |
cellx = simnfo->box_x / temp3; |
960 |
< |
celly = simnfo->box_y / temp3; |
961 |
< |
cellz = simnfo->box_z / temp3; |
962 |
< |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
963 |
< |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
964 |
< |
n_per_extra = (int)ceil( temp1 ); |
965 |
< |
|
966 |
< |
if( n_per_extra > 4){ |
967 |
< |
sprintf( painCave.errMsg, |
968 |
< |
"SimSetup error. There has been an error in constructing" |
969 |
< |
" the non-complete lattice.\n" ); |
970 |
< |
painCave.isFatal = 1; |
971 |
< |
simError(); |
655 |
> |
tot_nmol += the_components[i]->getNMol(); |
656 |
> |
components_nmol[i] = the_components[i]->getNMol(); |
657 |
|
} |
658 |
|
} |
659 |
|
else{ |
660 |
< |
n_cells = (int)temp3; |
661 |
< |
cellx = simnfo->box_x / temp3; |
662 |
< |
celly = simnfo->box_y / temp3; |
663 |
< |
cellz = simnfo->box_z / temp3; |
660 |
> |
sprintf(painCave.errMsg, |
661 |
> |
"SimSetup error.\n" |
662 |
> |
"\tSorry, the ability to specify total" |
663 |
> |
" nMols and then give molfractions in the components\n" |
664 |
> |
"\tis not currently supported." |
665 |
> |
" Please give nMol in the components.\n"); |
666 |
> |
painCave.isFatal = 1; |
667 |
> |
simError(); |
668 |
|
} |
669 |
|
|
670 |
< |
current_mol = 0; |
982 |
< |
current_comp_mol = 0; |
983 |
< |
current_comp = 0; |
984 |
< |
current_atom_ndx = 0; |
670 |
> |
// set the status, sample, and thermal kick times |
671 |
|
|
672 |
< |
for( i=0; i < n_cells ; i++ ){ |
673 |
< |
for( j=0; j < n_cells; j++ ){ |
674 |
< |
for( k=0; k < n_cells; k++ ){ |
672 |
> |
for (i = 0; i < nInfo; i++){ |
673 |
> |
if (globals->haveSampleTime()){ |
674 |
> |
info[i].sampleTime = globals->getSampleTime(); |
675 |
> |
info[i].statusTime = info[i].sampleTime; |
676 |
> |
info[i].thermalTime = info[i].sampleTime; |
677 |
> |
} |
678 |
> |
else{ |
679 |
> |
info[i].sampleTime = globals->getRunTime(); |
680 |
> |
info[i].statusTime = info[i].sampleTime; |
681 |
> |
info[i].thermalTime = info[i].sampleTime; |
682 |
> |
} |
683 |
|
|
684 |
< |
makeElement( i * cellx, |
685 |
< |
j * celly, |
686 |
< |
k * cellz ); |
684 |
> |
if (globals->haveStatusTime()){ |
685 |
> |
info[i].statusTime = globals->getStatusTime(); |
686 |
> |
} |
687 |
|
|
688 |
< |
makeElement( i * cellx + 0.5 * cellx, |
689 |
< |
j * celly + 0.5 * celly, |
690 |
< |
k * cellz ); |
688 |
> |
if (globals->haveThermalTime()){ |
689 |
> |
info[i].thermalTime = globals->getThermalTime(); |
690 |
> |
} |
691 |
|
|
692 |
< |
makeElement( i * cellx, |
693 |
< |
j * celly + 0.5 * celly, |
694 |
< |
k * cellz + 0.5 * cellz ); |
695 |
< |
|
1002 |
< |
makeElement( i * cellx + 0.5 * cellx, |
1003 |
< |
j * celly, |
1004 |
< |
k * cellz + 0.5 * cellz ); |
1005 |
< |
} |
692 |
> |
info[i].resetIntegrator = 0; |
693 |
> |
if( globals->haveResetTime() ){ |
694 |
> |
info[i].resetTime = globals->getResetTime(); |
695 |
> |
info[i].resetIntegrator = 1; |
696 |
|
} |
697 |
+ |
|
698 |
+ |
// check for the temperature set flag |
699 |
+ |
|
700 |
+ |
if (globals->haveTempSet()) |
701 |
+ |
info[i].setTemp = globals->getTempSet(); |
702 |
+ |
|
703 |
|
} |
704 |
+ |
|
705 |
+ |
//setup seed for random number generator |
706 |
+ |
int seedValue; |
707 |
|
|
708 |
< |
if( have_extra ){ |
709 |
< |
done = 0; |
708 |
> |
if (globals->haveSeed()){ |
709 |
> |
seedValue = globals->getSeed(); |
710 |
|
|
711 |
< |
int start_ndx; |
712 |
< |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
713 |
< |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
714 |
< |
|
715 |
< |
if( i < n_cells ){ |
711 |
> |
if(seedValue / 1E9 == 0){ |
712 |
> |
sprintf(painCave.errMsg, |
713 |
> |
"Seed for sprng library should contain at least 9 digits\n" |
714 |
> |
"OOPSE will generate a seed for user\n"); |
715 |
> |
painCave.isFatal = 0; |
716 |
> |
simError(); |
717 |
|
|
718 |
< |
if( j < n_cells ){ |
719 |
< |
start_ndx = n_cells; |
720 |
< |
} |
721 |
< |
else start_ndx = 0; |
722 |
< |
} |
723 |
< |
else start_ndx = 0; |
718 |
> |
//using seed generated by system instead of invalid seed set by user |
719 |
> |
#ifndef IS_MPI |
720 |
> |
seedValue = make_sprng_seed(); |
721 |
> |
#else |
722 |
> |
if (worldRank == 0){ |
723 |
> |
seedValue = make_sprng_seed(); |
724 |
> |
} |
725 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
726 |
> |
#endif |
727 |
> |
} |
728 |
> |
}//end of if branch of globals->haveSeed() |
729 |
> |
else{ |
730 |
> |
|
731 |
> |
#ifndef IS_MPI |
732 |
> |
seedValue = make_sprng_seed(); |
733 |
> |
#else |
734 |
> |
if (worldRank == 0){ |
735 |
> |
seedValue = make_sprng_seed(); |
736 |
> |
} |
737 |
> |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
738 |
> |
#endif |
739 |
> |
}//end of globals->haveSeed() |
740 |
|
|
741 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
741 |
> |
for (int i = 0; i < nInfo; i++){ |
742 |
> |
info[i].setSeed(seedValue); |
743 |
> |
} |
744 |
|
|
745 |
< |
makeElement( i * cellx, |
746 |
< |
j * celly, |
747 |
< |
k * cellz ); |
748 |
< |
done = ( current_mol >= tot_nmol ); |
745 |
> |
#ifdef IS_MPI |
746 |
> |
strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
747 |
> |
MPIcheckPoint(); |
748 |
> |
#endif // is_mpi |
749 |
> |
} |
750 |
|
|
1032 |
– |
if( !done && n_per_extra > 1 ){ |
1033 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1034 |
– |
j * celly + 0.5 * celly, |
1035 |
– |
k * cellz ); |
1036 |
– |
done = ( current_mol >= tot_nmol ); |
1037 |
– |
} |
751 |
|
|
752 |
< |
if( !done && n_per_extra > 2){ |
753 |
< |
makeElement( i * cellx, |
754 |
< |
j * celly + 0.5 * celly, |
755 |
< |
k * cellz + 0.5 * cellz ); |
1043 |
< |
done = ( current_mol >= tot_nmol ); |
1044 |
< |
} |
752 |
> |
void SimSetup::finalInfoCheck(void){ |
753 |
> |
int index; |
754 |
> |
int usesDipoles; |
755 |
> |
int i; |
756 |
|
|
757 |
< |
if( !done && n_per_extra > 3){ |
758 |
< |
makeElement( i * cellx + 0.5 * cellx, |
759 |
< |
j * celly, |
760 |
< |
k * cellz + 0.5 * cellz ); |
761 |
< |
done = ( current_mol >= tot_nmol ); |
762 |
< |
} |
763 |
< |
} |
757 |
> |
for (i = 0; i < nInfo; i++){ |
758 |
> |
// check electrostatic parameters |
759 |
> |
|
760 |
> |
index = 0; |
761 |
> |
usesDipoles = 0; |
762 |
> |
while ((index < info[i].n_atoms) && !usesDipoles){ |
763 |
> |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
764 |
> |
index++; |
765 |
> |
} |
766 |
> |
|
767 |
> |
#ifdef IS_MPI |
768 |
> |
int myUse = usesDipoles; |
769 |
> |
MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
770 |
> |
#endif //is_mpi |
771 |
> |
|
772 |
> |
double theEcr, theEst; |
773 |
> |
|
774 |
> |
if (globals->getUseRF()){ |
775 |
> |
info[i].useReactionField = 1; |
776 |
> |
|
777 |
> |
if (!globals->haveECR()){ |
778 |
> |
sprintf(painCave.errMsg, |
779 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
780 |
> |
"box length for the electrostaticCutoffRadius.\n" |
781 |
> |
"I hope you have a very fast processor!\n"); |
782 |
> |
painCave.isFatal = 0; |
783 |
> |
simError(); |
784 |
> |
double smallest; |
785 |
> |
smallest = info[i].boxL[0]; |
786 |
> |
if (info[i].boxL[1] <= smallest) |
787 |
> |
smallest = info[i].boxL[1]; |
788 |
> |
if (info[i].boxL[2] <= smallest) |
789 |
> |
smallest = info[i].boxL[2]; |
790 |
> |
theEcr = 0.5 * smallest; |
791 |
|
} |
792 |
+ |
else{ |
793 |
+ |
theEcr = globals->getECR(); |
794 |
+ |
} |
795 |
+ |
|
796 |
+ |
if (!globals->haveEST()){ |
797 |
+ |
sprintf(painCave.errMsg, |
798 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
799 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
800 |
+ |
painCave.isFatal = 0; |
801 |
+ |
simError(); |
802 |
+ |
theEst = 0.05 * theEcr; |
803 |
+ |
} |
804 |
+ |
else{ |
805 |
+ |
theEst = globals->getEST(); |
806 |
+ |
} |
807 |
+ |
|
808 |
+ |
info[i].setDefaultEcr(theEcr, theEst); |
809 |
+ |
|
810 |
+ |
if (!globals->haveDielectric()){ |
811 |
+ |
sprintf(painCave.errMsg, |
812 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
813 |
+ |
"setting a dielectric constant!\n"); |
814 |
+ |
painCave.isFatal = 1; |
815 |
+ |
simError(); |
816 |
+ |
} |
817 |
+ |
info[i].dielectric = globals->getDielectric(); |
818 |
|
} |
819 |
+ |
else{ |
820 |
+ |
if (usesDipoles){ |
821 |
+ |
if (!globals->haveECR()){ |
822 |
+ |
sprintf(painCave.errMsg, |
823 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
824 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
825 |
+ |
"I hope you have a very fast processor!\n"); |
826 |
+ |
painCave.isFatal = 0; |
827 |
+ |
simError(); |
828 |
+ |
double smallest; |
829 |
+ |
smallest = info[i].boxL[0]; |
830 |
+ |
if (info[i].boxL[1] <= smallest) |
831 |
+ |
smallest = info[i].boxL[1]; |
832 |
+ |
if (info[i].boxL[2] <= smallest) |
833 |
+ |
smallest = info[i].boxL[2]; |
834 |
+ |
theEcr = 0.5 * smallest; |
835 |
+ |
} |
836 |
+ |
else{ |
837 |
+ |
theEcr = globals->getECR(); |
838 |
+ |
} |
839 |
+ |
|
840 |
+ |
if (!globals->haveEST()){ |
841 |
+ |
sprintf(painCave.errMsg, |
842 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
843 |
+ |
"electrostaticCutoffRadius for the " |
844 |
+ |
"electrostaticSkinThickness\n"); |
845 |
+ |
painCave.isFatal = 0; |
846 |
+ |
simError(); |
847 |
+ |
theEst = 0.05 * theEcr; |
848 |
+ |
} |
849 |
+ |
else{ |
850 |
+ |
theEst = globals->getEST(); |
851 |
+ |
} |
852 |
+ |
|
853 |
+ |
info[i].setDefaultEcr(theEcr, theEst); |
854 |
+ |
} |
855 |
+ |
} |
856 |
|
} |
857 |
|
|
858 |
+ |
#ifdef IS_MPI |
859 |
+ |
strcpy(checkPointMsg, "post processing checks out"); |
860 |
+ |
MPIcheckPoint(); |
861 |
+ |
#endif // is_mpi |
862 |
+ |
} |
863 |
|
|
864 |
< |
for( i=0; i<simnfo->n_atoms; i++ ){ |
865 |
< |
simnfo->atoms[i]->set_vx( 0.0 ); |
866 |
< |
simnfo->atoms[i]->set_vy( 0.0 ); |
867 |
< |
simnfo->atoms[i]->set_vz( 0.0 ); |
864 |
> |
void SimSetup::initSystemCoords(void){ |
865 |
> |
int i; |
866 |
> |
|
867 |
> |
char* inName; |
868 |
> |
|
869 |
> |
(info[0].getConfiguration())->createArrays(info[0].n_atoms); |
870 |
> |
|
871 |
> |
for (i = 0; i < info[0].n_atoms; i++) |
872 |
> |
info[0].atoms[i]->setCoords(); |
873 |
> |
|
874 |
> |
if (globals->haveInitialConfig()){ |
875 |
> |
InitializeFromFile* fileInit; |
876 |
> |
#ifdef IS_MPI // is_mpi |
877 |
> |
if (worldRank == 0){ |
878 |
> |
#endif //is_mpi |
879 |
> |
inName = globals->getInitialConfig(); |
880 |
> |
fileInit = new InitializeFromFile(inName); |
881 |
> |
#ifdef IS_MPI |
882 |
> |
} |
883 |
> |
else |
884 |
> |
fileInit = new InitializeFromFile(NULL); |
885 |
> |
#endif |
886 |
> |
fileInit->readInit(info); // default velocities on |
887 |
> |
|
888 |
> |
delete fileInit; |
889 |
|
} |
890 |
+ |
else{ |
891 |
+ |
#ifdef IS_MPI |
892 |
+ |
|
893 |
+ |
// no init from bass |
894 |
+ |
|
895 |
+ |
sprintf(painCave.errMsg, |
896 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
897 |
+ |
painCave.isFatal = 1;; |
898 |
+ |
simError(); |
899 |
+ |
|
900 |
+ |
#else |
901 |
+ |
|
902 |
+ |
initFromBass(); |
903 |
+ |
|
904 |
+ |
|
905 |
+ |
#endif |
906 |
+ |
} |
907 |
+ |
|
908 |
+ |
#ifdef IS_MPI |
909 |
+ |
strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
910 |
+ |
MPIcheckPoint(); |
911 |
+ |
#endif // is_mpi |
912 |
|
} |
913 |
|
|
1065 |
– |
void SimSetup::makeElement( double x, double y, double z ){ |
914 |
|
|
915 |
+ |
void SimSetup::makeOutNames(void){ |
916 |
|
int k; |
1068 |
– |
AtomStamp* current_atom; |
1069 |
– |
DirectionalAtom* dAtom; |
1070 |
– |
double rotMat[3][3]; |
917 |
|
|
1072 |
– |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
918 |
|
|
919 |
< |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
920 |
< |
if( !current_atom->havePosition() ){ |
921 |
< |
sprintf( painCave.errMsg, |
922 |
< |
"SimSetup:initFromBass error.\n" |
923 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
924 |
< |
"\tThe initialization routine is unable to give a start" |
925 |
< |
" position.\n", |
926 |
< |
comp_stamps[current_comp]->getID(), |
927 |
< |
current_atom->getType() ); |
919 |
> |
for (k = 0; k < nInfo; k++){ |
920 |
> |
#ifdef IS_MPI |
921 |
> |
if (worldRank == 0){ |
922 |
> |
#endif // is_mpi |
923 |
> |
|
924 |
> |
if (globals->haveFinalConfig()){ |
925 |
> |
strcpy(info[k].finalName, globals->getFinalConfig()); |
926 |
> |
} |
927 |
> |
else{ |
928 |
> |
strcpy(info[k].finalName, inFileName); |
929 |
> |
char* endTest; |
930 |
> |
int nameLength = strlen(info[k].finalName); |
931 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
932 |
> |
if (!strcmp(endTest, ".bass")){ |
933 |
> |
strcpy(endTest, ".eor"); |
934 |
> |
} |
935 |
> |
else if (!strcmp(endTest, ".BASS")){ |
936 |
> |
strcpy(endTest, ".eor"); |
937 |
> |
} |
938 |
> |
else{ |
939 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
940 |
> |
if (!strcmp(endTest, ".bss")){ |
941 |
> |
strcpy(endTest, ".eor"); |
942 |
> |
} |
943 |
> |
else if (!strcmp(endTest, ".mdl")){ |
944 |
> |
strcpy(endTest, ".eor"); |
945 |
> |
} |
946 |
> |
else{ |
947 |
> |
strcat(info[k].finalName, ".eor"); |
948 |
> |
} |
949 |
> |
} |
950 |
> |
} |
951 |
> |
|
952 |
> |
// make the sample and status out names |
953 |
> |
|
954 |
> |
strcpy(info[k].sampleName, inFileName); |
955 |
> |
char* endTest; |
956 |
> |
int nameLength = strlen(info[k].sampleName); |
957 |
> |
endTest = &(info[k].sampleName[nameLength - 5]); |
958 |
> |
if (!strcmp(endTest, ".bass")){ |
959 |
> |
strcpy(endTest, ".dump"); |
960 |
> |
} |
961 |
> |
else if (!strcmp(endTest, ".BASS")){ |
962 |
> |
strcpy(endTest, ".dump"); |
963 |
> |
} |
964 |
> |
else{ |
965 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
966 |
> |
if (!strcmp(endTest, ".bss")){ |
967 |
> |
strcpy(endTest, ".dump"); |
968 |
> |
} |
969 |
> |
else if (!strcmp(endTest, ".mdl")){ |
970 |
> |
strcpy(endTest, ".dump"); |
971 |
> |
} |
972 |
> |
else{ |
973 |
> |
strcat(info[k].sampleName, ".dump"); |
974 |
> |
} |
975 |
> |
} |
976 |
> |
|
977 |
> |
strcpy(info[k].statusName, inFileName); |
978 |
> |
nameLength = strlen(info[k].statusName); |
979 |
> |
endTest = &(info[k].statusName[nameLength - 5]); |
980 |
> |
if (!strcmp(endTest, ".bass")){ |
981 |
> |
strcpy(endTest, ".stat"); |
982 |
> |
} |
983 |
> |
else if (!strcmp(endTest, ".BASS")){ |
984 |
> |
strcpy(endTest, ".stat"); |
985 |
> |
} |
986 |
> |
else{ |
987 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
988 |
> |
if (!strcmp(endTest, ".bss")){ |
989 |
> |
strcpy(endTest, ".stat"); |
990 |
> |
} |
991 |
> |
else if (!strcmp(endTest, ".mdl")){ |
992 |
> |
strcpy(endTest, ".stat"); |
993 |
> |
} |
994 |
> |
else{ |
995 |
> |
strcat(info[k].statusName, ".stat"); |
996 |
> |
} |
997 |
> |
} |
998 |
> |
|
999 |
> |
#ifdef IS_MPI |
1000 |
> |
|
1001 |
> |
} |
1002 |
> |
#endif // is_mpi |
1003 |
> |
} |
1004 |
> |
} |
1005 |
> |
|
1006 |
> |
|
1007 |
> |
void SimSetup::sysObjectsCreation(void){ |
1008 |
> |
int i, k; |
1009 |
> |
|
1010 |
> |
// create the forceField |
1011 |
> |
|
1012 |
> |
createFF(); |
1013 |
> |
|
1014 |
> |
// extract componentList |
1015 |
> |
|
1016 |
> |
compList(); |
1017 |
> |
|
1018 |
> |
// calc the number of atoms, bond, bends, and torsions |
1019 |
> |
|
1020 |
> |
calcSysValues(); |
1021 |
> |
|
1022 |
> |
#ifdef IS_MPI |
1023 |
> |
// divide the molecules among the processors |
1024 |
> |
|
1025 |
> |
mpiMolDivide(); |
1026 |
> |
#endif //is_mpi |
1027 |
> |
|
1028 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1029 |
> |
|
1030 |
> |
makeSysArrays(); |
1031 |
> |
|
1032 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1033 |
> |
|
1034 |
> |
makeMolecules(); |
1035 |
> |
|
1036 |
> |
for (k = 0; k < nInfo; k++){ |
1037 |
> |
info[k].identArray = new int[info[k].n_atoms]; |
1038 |
> |
for (i = 0; i < info[k].n_atoms; i++){ |
1039 |
> |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1040 |
> |
} |
1041 |
> |
} |
1042 |
> |
} |
1043 |
> |
|
1044 |
> |
|
1045 |
> |
void SimSetup::createFF(void){ |
1046 |
> |
switch (ffCase){ |
1047 |
> |
case FF_DUFF: |
1048 |
> |
the_ff = new DUFF(); |
1049 |
> |
break; |
1050 |
> |
|
1051 |
> |
case FF_LJ: |
1052 |
> |
the_ff = new LJFF(); |
1053 |
> |
break; |
1054 |
> |
|
1055 |
> |
case FF_EAM: |
1056 |
> |
the_ff = new EAM_FF(); |
1057 |
> |
break; |
1058 |
> |
|
1059 |
> |
default: |
1060 |
> |
sprintf(painCave.errMsg, |
1061 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1062 |
|
painCave.isFatal = 1; |
1063 |
|
simError(); |
1064 |
+ |
} |
1065 |
+ |
|
1066 |
+ |
#ifdef IS_MPI |
1067 |
+ |
strcpy(checkPointMsg, "ForceField creation successful"); |
1068 |
+ |
MPIcheckPoint(); |
1069 |
+ |
#endif // is_mpi |
1070 |
+ |
} |
1071 |
+ |
|
1072 |
+ |
|
1073 |
+ |
void SimSetup::compList(void){ |
1074 |
+ |
int i; |
1075 |
+ |
char* id; |
1076 |
+ |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1077 |
+ |
LinkedMolStamp* currentStamp = NULL; |
1078 |
+ |
comp_stamps = new MoleculeStamp * [n_components]; |
1079 |
+ |
|
1080 |
+ |
// make an array of molecule stamps that match the components used. |
1081 |
+ |
// also extract the used stamps out into a separate linked list |
1082 |
+ |
|
1083 |
+ |
for (i = 0; i < nInfo; i++){ |
1084 |
+ |
info[i].nComponents = n_components; |
1085 |
+ |
info[i].componentsNmol = components_nmol; |
1086 |
+ |
info[i].compStamps = comp_stamps; |
1087 |
+ |
info[i].headStamp = headStamp; |
1088 |
+ |
} |
1089 |
+ |
|
1090 |
+ |
|
1091 |
+ |
for (i = 0; i < n_components; i++){ |
1092 |
+ |
id = the_components[i]->getType(); |
1093 |
+ |
comp_stamps[i] = NULL; |
1094 |
+ |
|
1095 |
+ |
// check to make sure the component isn't already in the list |
1096 |
+ |
|
1097 |
+ |
comp_stamps[i] = headStamp->match(id); |
1098 |
+ |
if (comp_stamps[i] == NULL){ |
1099 |
+ |
// extract the component from the list; |
1100 |
+ |
|
1101 |
+ |
currentStamp = stamps->extractMolStamp(id); |
1102 |
+ |
if (currentStamp == NULL){ |
1103 |
+ |
sprintf(painCave.errMsg, |
1104 |
+ |
"SimSetup error: Component \"%s\" was not found in the " |
1105 |
+ |
"list of declared molecules\n", |
1106 |
+ |
id); |
1107 |
+ |
painCave.isFatal = 1; |
1108 |
+ |
simError(); |
1109 |
+ |
} |
1110 |
+ |
|
1111 |
+ |
headStamp->add(currentStamp); |
1112 |
+ |
comp_stamps[i] = headStamp->match(id); |
1113 |
|
} |
1114 |
+ |
} |
1115 |
|
|
1116 |
< |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1117 |
< |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1118 |
< |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1116 |
> |
#ifdef IS_MPI |
1117 |
> |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1118 |
> |
MPIcheckPoint(); |
1119 |
> |
#endif // is_mpi |
1120 |
> |
} |
1121 |
|
|
1122 |
< |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1122 |
> |
void SimSetup::calcSysValues(void){ |
1123 |
> |
int i; |
1124 |
|
|
1125 |
< |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1125 |
> |
int* molMembershipArray; |
1126 |
|
|
1127 |
< |
rotMat[0][0] = 1.0; |
1128 |
< |
rotMat[0][1] = 0.0; |
1129 |
< |
rotMat[0][2] = 0.0; |
1127 |
> |
tot_atoms = 0; |
1128 |
> |
tot_bonds = 0; |
1129 |
> |
tot_bends = 0; |
1130 |
> |
tot_torsions = 0; |
1131 |
> |
for (i = 0; i < n_components; i++){ |
1132 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1133 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1134 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1135 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1136 |
> |
} |
1137 |
|
|
1138 |
< |
rotMat[1][0] = 0.0; |
1139 |
< |
rotMat[1][1] = 1.0; |
1101 |
< |
rotMat[1][2] = 0.0; |
1138 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1139 |
> |
molMembershipArray = new int[tot_atoms]; |
1140 |
|
|
1141 |
< |
rotMat[2][0] = 0.0; |
1142 |
< |
rotMat[2][1] = 0.0; |
1143 |
< |
rotMat[2][2] = 1.0; |
1141 |
> |
for (i = 0; i < nInfo; i++){ |
1142 |
> |
info[i].n_atoms = tot_atoms; |
1143 |
> |
info[i].n_bonds = tot_bonds; |
1144 |
> |
info[i].n_bends = tot_bends; |
1145 |
> |
info[i].n_torsions = tot_torsions; |
1146 |
> |
info[i].n_SRI = tot_SRI; |
1147 |
> |
info[i].n_mol = tot_nmol; |
1148 |
|
|
1149 |
< |
dAtom->setA( rotMat ); |
1149 |
> |
info[i].molMembershipArray = molMembershipArray; |
1150 |
> |
} |
1151 |
> |
} |
1152 |
> |
|
1153 |
> |
#ifdef IS_MPI |
1154 |
> |
|
1155 |
> |
void SimSetup::mpiMolDivide(void){ |
1156 |
> |
int i, j, k; |
1157 |
> |
int localMol, allMol; |
1158 |
> |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1159 |
> |
|
1160 |
> |
mpiSim = new mpiSimulation(info); |
1161 |
> |
|
1162 |
> |
globalIndex = mpiSim->divideLabor(); |
1163 |
> |
|
1164 |
> |
// set up the local variables |
1165 |
> |
|
1166 |
> |
mol2proc = mpiSim->getMolToProcMap(); |
1167 |
> |
molCompType = mpiSim->getMolComponentType(); |
1168 |
> |
|
1169 |
> |
allMol = 0; |
1170 |
> |
localMol = 0; |
1171 |
> |
local_atoms = 0; |
1172 |
> |
local_bonds = 0; |
1173 |
> |
local_bends = 0; |
1174 |
> |
local_torsions = 0; |
1175 |
> |
globalAtomIndex = 0; |
1176 |
> |
|
1177 |
> |
|
1178 |
> |
for (i = 0; i < n_components; i++){ |
1179 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1180 |
> |
if (mol2proc[allMol] == worldRank){ |
1181 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1182 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1183 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1184 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1185 |
> |
localMol++; |
1186 |
> |
} |
1187 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1188 |
> |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1189 |
> |
globalAtomIndex++; |
1190 |
> |
} |
1191 |
> |
|
1192 |
> |
allMol++; |
1193 |
|
} |
1194 |
+ |
} |
1195 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1196 |
|
|
1197 |
< |
current_atom_ndx++; |
1197 |
> |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1198 |
> |
|
1199 |
> |
if (local_atoms != info[0].n_atoms){ |
1200 |
> |
sprintf(painCave.errMsg, |
1201 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1202 |
> |
" localAtom (%d) are not equal.\n", |
1203 |
> |
info[0].n_atoms, local_atoms); |
1204 |
> |
painCave.isFatal = 1; |
1205 |
> |
simError(); |
1206 |
|
} |
1207 |
|
|
1208 |
< |
current_mol++; |
1209 |
< |
current_comp_mol++; |
1208 |
> |
info[0].n_bonds = local_bonds; |
1209 |
> |
info[0].n_bends = local_bends; |
1210 |
> |
info[0].n_torsions = local_torsions; |
1211 |
> |
info[0].n_SRI = local_SRI; |
1212 |
> |
info[0].n_mol = localMol; |
1213 |
|
|
1214 |
< |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1214 |
> |
strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1215 |
> |
MPIcheckPoint(); |
1216 |
> |
} |
1217 |
|
|
1218 |
< |
current_comp_mol = 0; |
1219 |
< |
current_comp++; |
1218 |
> |
#endif // is_mpi |
1219 |
> |
|
1220 |
> |
|
1221 |
> |
void SimSetup::makeSysArrays(void){ |
1222 |
> |
|
1223 |
> |
#ifndef IS_MPI |
1224 |
> |
int k, j; |
1225 |
> |
#endif // is_mpi |
1226 |
> |
int i, l; |
1227 |
> |
|
1228 |
> |
Atom** the_atoms; |
1229 |
> |
Molecule* the_molecules; |
1230 |
> |
Exclude** the_excludes; |
1231 |
> |
|
1232 |
> |
|
1233 |
> |
for (l = 0; l < nInfo; l++){ |
1234 |
> |
// create the atom and short range interaction arrays |
1235 |
> |
|
1236 |
> |
the_atoms = new Atom * [info[l].n_atoms]; |
1237 |
> |
the_molecules = new Molecule[info[l].n_mol]; |
1238 |
> |
int molIndex; |
1239 |
> |
|
1240 |
> |
// initialize the molecule's stampID's |
1241 |
> |
|
1242 |
> |
#ifdef IS_MPI |
1243 |
> |
|
1244 |
> |
|
1245 |
> |
molIndex = 0; |
1246 |
> |
for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1247 |
> |
if (mol2proc[i] == worldRank){ |
1248 |
> |
the_molecules[molIndex].setStampID(molCompType[i]); |
1249 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1250 |
> |
the_molecules[molIndex].setGlobalIndex(i); |
1251 |
> |
molIndex++; |
1252 |
> |
} |
1253 |
> |
} |
1254 |
> |
|
1255 |
> |
#else // is_mpi |
1256 |
> |
|
1257 |
> |
molIndex = 0; |
1258 |
> |
globalAtomIndex = 0; |
1259 |
> |
for (i = 0; i < n_components; i++){ |
1260 |
> |
for (j = 0; j < components_nmol[i]; j++){ |
1261 |
> |
the_molecules[molIndex].setStampID(i); |
1262 |
> |
the_molecules[molIndex].setMyIndex(molIndex); |
1263 |
> |
the_molecules[molIndex].setGlobalIndex(molIndex); |
1264 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1265 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1266 |
> |
globalAtomIndex++; |
1267 |
> |
} |
1268 |
> |
molIndex++; |
1269 |
> |
} |
1270 |
> |
} |
1271 |
> |
|
1272 |
> |
|
1273 |
> |
#endif // is_mpi |
1274 |
> |
|
1275 |
> |
|
1276 |
> |
if (info[l].n_SRI){ |
1277 |
> |
Exclude::createArray(info[l].n_SRI); |
1278 |
> |
the_excludes = new Exclude * [info[l].n_SRI]; |
1279 |
> |
for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1280 |
> |
the_excludes[ex] = new Exclude(ex); |
1281 |
> |
} |
1282 |
> |
info[l].globalExcludes = new int; |
1283 |
> |
info[l].n_exclude = info[l].n_SRI; |
1284 |
> |
} |
1285 |
> |
else{ |
1286 |
> |
Exclude::createArray(1); |
1287 |
> |
the_excludes = new Exclude * ; |
1288 |
> |
the_excludes[0] = new Exclude(0); |
1289 |
> |
the_excludes[0]->setPair(0, 0); |
1290 |
> |
info[l].globalExcludes = new int; |
1291 |
> |
info[l].globalExcludes[0] = 0; |
1292 |
> |
info[l].n_exclude = 0; |
1293 |
> |
} |
1294 |
> |
|
1295 |
> |
// set the arrays into the SimInfo object |
1296 |
> |
|
1297 |
> |
info[l].atoms = the_atoms; |
1298 |
> |
info[l].molecules = the_molecules; |
1299 |
> |
info[l].nGlobalExcludes = 0; |
1300 |
> |
info[l].excludes = the_excludes; |
1301 |
> |
|
1302 |
> |
the_ff->setSimInfo(info); |
1303 |
> |
} |
1304 |
> |
} |
1305 |
> |
|
1306 |
> |
void SimSetup::makeIntegrator(void){ |
1307 |
> |
int k; |
1308 |
> |
|
1309 |
> |
NVE<RealIntegrator>* myNVE = NULL; |
1310 |
> |
NVT<RealIntegrator>* myNVT = NULL; |
1311 |
> |
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1312 |
> |
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1313 |
> |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1314 |
> |
|
1315 |
> |
for (k = 0; k < nInfo; k++){ |
1316 |
> |
switch (ensembleCase){ |
1317 |
> |
case NVE_ENS: |
1318 |
> |
if (globals->haveZconstraints()){ |
1319 |
> |
setupZConstraint(info[k]); |
1320 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1321 |
> |
} |
1322 |
> |
else{ |
1323 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1324 |
> |
} |
1325 |
> |
|
1326 |
> |
info->the_integrator = myNVE; |
1327 |
> |
break; |
1328 |
> |
|
1329 |
> |
case NVT_ENS: |
1330 |
> |
if (globals->haveZconstraints()){ |
1331 |
> |
setupZConstraint(info[k]); |
1332 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1333 |
> |
} |
1334 |
> |
else |
1335 |
> |
myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1336 |
> |
|
1337 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1338 |
> |
|
1339 |
> |
if (globals->haveTauThermostat()) |
1340 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1341 |
> |
else{ |
1342 |
> |
sprintf(painCave.errMsg, |
1343 |
> |
"SimSetup error: If you use the NVT\n" |
1344 |
> |
" ensemble, you must set tauThermostat.\n"); |
1345 |
> |
painCave.isFatal = 1; |
1346 |
> |
simError(); |
1347 |
> |
} |
1348 |
> |
|
1349 |
> |
info->the_integrator = myNVT; |
1350 |
> |
break; |
1351 |
> |
|
1352 |
> |
case NPTi_ENS: |
1353 |
> |
if (globals->haveZconstraints()){ |
1354 |
> |
setupZConstraint(info[k]); |
1355 |
> |
myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1356 |
> |
} |
1357 |
> |
else |
1358 |
> |
myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1359 |
> |
|
1360 |
> |
myNPTi->setTargetTemp(globals->getTargetTemp()); |
1361 |
> |
|
1362 |
> |
if (globals->haveTargetPressure()) |
1363 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1364 |
> |
else{ |
1365 |
> |
sprintf(painCave.errMsg, |
1366 |
> |
"SimSetup error: If you use a constant pressure\n" |
1367 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1368 |
> |
painCave.isFatal = 1; |
1369 |
> |
simError(); |
1370 |
> |
} |
1371 |
> |
|
1372 |
> |
if (globals->haveTauThermostat()) |
1373 |
> |
myNPTi->setTauThermostat(globals->getTauThermostat()); |
1374 |
> |
else{ |
1375 |
> |
sprintf(painCave.errMsg, |
1376 |
> |
"SimSetup error: If you use an NPT\n" |
1377 |
> |
" ensemble, you must set tauThermostat.\n"); |
1378 |
> |
painCave.isFatal = 1; |
1379 |
> |
simError(); |
1380 |
> |
} |
1381 |
> |
|
1382 |
> |
if (globals->haveTauBarostat()) |
1383 |
> |
myNPTi->setTauBarostat(globals->getTauBarostat()); |
1384 |
> |
else{ |
1385 |
> |
sprintf(painCave.errMsg, |
1386 |
> |
"SimSetup error: If you use an NPT\n" |
1387 |
> |
" ensemble, you must set tauBarostat.\n"); |
1388 |
> |
painCave.isFatal = 1; |
1389 |
> |
simError(); |
1390 |
> |
} |
1391 |
> |
|
1392 |
> |
info->the_integrator = myNPTi; |
1393 |
> |
break; |
1394 |
> |
|
1395 |
> |
case NPTf_ENS: |
1396 |
> |
if (globals->haveZconstraints()){ |
1397 |
> |
setupZConstraint(info[k]); |
1398 |
> |
myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1399 |
> |
} |
1400 |
> |
else |
1401 |
> |
myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1402 |
> |
|
1403 |
> |
myNPTf->setTargetTemp(globals->getTargetTemp()); |
1404 |
> |
|
1405 |
> |
if (globals->haveTargetPressure()) |
1406 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1407 |
> |
else{ |
1408 |
> |
sprintf(painCave.errMsg, |
1409 |
> |
"SimSetup error: If you use a constant pressure\n" |
1410 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
> |
painCave.isFatal = 1; |
1412 |
> |
simError(); |
1413 |
> |
} |
1414 |
> |
|
1415 |
> |
if (globals->haveTauThermostat()) |
1416 |
> |
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1417 |
> |
else{ |
1418 |
> |
sprintf(painCave.errMsg, |
1419 |
> |
"SimSetup error: If you use an NPT\n" |
1420 |
> |
" ensemble, you must set tauThermostat.\n"); |
1421 |
> |
painCave.isFatal = 1; |
1422 |
> |
simError(); |
1423 |
> |
} |
1424 |
> |
|
1425 |
> |
if (globals->haveTauBarostat()) |
1426 |
> |
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1427 |
> |
else{ |
1428 |
> |
sprintf(painCave.errMsg, |
1429 |
> |
"SimSetup error: If you use an NPT\n" |
1430 |
> |
" ensemble, you must set tauBarostat.\n"); |
1431 |
> |
painCave.isFatal = 1; |
1432 |
> |
simError(); |
1433 |
> |
} |
1434 |
> |
|
1435 |
> |
info->the_integrator = myNPTf; |
1436 |
> |
break; |
1437 |
> |
|
1438 |
> |
case NPTxyz_ENS: |
1439 |
> |
if (globals->haveZconstraints()){ |
1440 |
> |
setupZConstraint(info[k]); |
1441 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1442 |
> |
} |
1443 |
> |
else |
1444 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1445 |
> |
|
1446 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1447 |
> |
|
1448 |
> |
if (globals->haveTargetPressure()) |
1449 |
> |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1450 |
> |
else{ |
1451 |
> |
sprintf(painCave.errMsg, |
1452 |
> |
"SimSetup error: If you use a constant pressure\n" |
1453 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1454 |
> |
painCave.isFatal = 1; |
1455 |
> |
simError(); |
1456 |
> |
} |
1457 |
> |
|
1458 |
> |
if (globals->haveTauThermostat()) |
1459 |
> |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1460 |
> |
else{ |
1461 |
> |
sprintf(painCave.errMsg, |
1462 |
> |
"SimSetup error: If you use an NPT\n" |
1463 |
> |
" ensemble, you must set tauThermostat.\n"); |
1464 |
> |
painCave.isFatal = 1; |
1465 |
> |
simError(); |
1466 |
> |
} |
1467 |
> |
|
1468 |
> |
if (globals->haveTauBarostat()) |
1469 |
> |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1470 |
> |
else{ |
1471 |
> |
sprintf(painCave.errMsg, |
1472 |
> |
"SimSetup error: If you use an NPT\n" |
1473 |
> |
" ensemble, you must set tauBarostat.\n"); |
1474 |
> |
painCave.isFatal = 1; |
1475 |
> |
simError(); |
1476 |
> |
} |
1477 |
> |
|
1478 |
> |
info->the_integrator = myNPTxyz; |
1479 |
> |
break; |
1480 |
> |
|
1481 |
> |
default: |
1482 |
> |
sprintf(painCave.errMsg, |
1483 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1484 |
> |
painCave.isFatal = 1; |
1485 |
> |
simError(); |
1486 |
> |
} |
1487 |
|
} |
1488 |
|
} |
1489 |
+ |
|
1490 |
+ |
void SimSetup::initFortran(void){ |
1491 |
+ |
info[0].refreshSim(); |
1492 |
+ |
|
1493 |
+ |
if (!strcmp(info[0].mixingRule, "standard")){ |
1494 |
+ |
the_ff->initForceField(LB_MIXING_RULE); |
1495 |
+ |
} |
1496 |
+ |
else if (!strcmp(info[0].mixingRule, "explicit")){ |
1497 |
+ |
the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1498 |
+ |
} |
1499 |
+ |
else{ |
1500 |
+ |
sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1501 |
+ |
info[0].mixingRule); |
1502 |
+ |
painCave.isFatal = 1; |
1503 |
+ |
simError(); |
1504 |
+ |
} |
1505 |
+ |
|
1506 |
+ |
|
1507 |
+ |
#ifdef IS_MPI |
1508 |
+ |
strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1509 |
+ |
MPIcheckPoint(); |
1510 |
+ |
#endif // is_mpi |
1511 |
+ |
} |
1512 |
+ |
|
1513 |
+ |
void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1514 |
+ |
int nZConstraints; |
1515 |
+ |
ZconStamp** zconStamp; |
1516 |
+ |
|
1517 |
+ |
if (globals->haveZconstraintTime()){ |
1518 |
+ |
//add sample time of z-constraint into SimInfo's property list |
1519 |
+ |
DoubleData* zconsTimeProp = new DoubleData(); |
1520 |
+ |
zconsTimeProp->setID(ZCONSTIME_ID); |
1521 |
+ |
zconsTimeProp->setData(globals->getZconsTime()); |
1522 |
+ |
theInfo.addProperty(zconsTimeProp); |
1523 |
+ |
} |
1524 |
+ |
else{ |
1525 |
+ |
sprintf(painCave.errMsg, |
1526 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
1527 |
+ |
" , you must set sample time.\n"); |
1528 |
+ |
painCave.isFatal = 1; |
1529 |
+ |
simError(); |
1530 |
+ |
} |
1531 |
+ |
|
1532 |
+ |
//push zconsTol into siminfo, if user does not specify |
1533 |
+ |
//value for zconsTol, a default value will be used |
1534 |
+ |
DoubleData* zconsTol = new DoubleData(); |
1535 |
+ |
zconsTol->setID(ZCONSTOL_ID); |
1536 |
+ |
if (globals->haveZconsTol()){ |
1537 |
+ |
zconsTol->setData(globals->getZconsTol()); |
1538 |
+ |
} |
1539 |
+ |
else{ |
1540 |
+ |
double defaultZConsTol = 0.01; |
1541 |
+ |
sprintf(painCave.errMsg, |
1542 |
+ |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1543 |
+ |
" , default value %f is used.\n", |
1544 |
+ |
defaultZConsTol); |
1545 |
+ |
painCave.isFatal = 0; |
1546 |
+ |
simError(); |
1547 |
+ |
|
1548 |
+ |
zconsTol->setData(defaultZConsTol); |
1549 |
+ |
} |
1550 |
+ |
theInfo.addProperty(zconsTol); |
1551 |
+ |
|
1552 |
+ |
//set Force Subtraction Policy |
1553 |
+ |
StringData* zconsForcePolicy = new StringData(); |
1554 |
+ |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1555 |
+ |
|
1556 |
+ |
if (globals->haveZconsForcePolicy()){ |
1557 |
+ |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1558 |
+ |
} |
1559 |
+ |
else{ |
1560 |
+ |
sprintf(painCave.errMsg, |
1561 |
+ |
"ZConstraint Warning: User does not set force Subtraction policy, " |
1562 |
+ |
"PolicyByMass is used\n"); |
1563 |
+ |
painCave.isFatal = 0; |
1564 |
+ |
simError(); |
1565 |
+ |
zconsForcePolicy->setData("BYMASS"); |
1566 |
+ |
} |
1567 |
+ |
|
1568 |
+ |
theInfo.addProperty(zconsForcePolicy); |
1569 |
+ |
|
1570 |
+ |
//Determine the name of ouput file and add it into SimInfo's property list |
1571 |
+ |
//Be careful, do not use inFileName, since it is a pointer which |
1572 |
+ |
//point to a string at master node, and slave nodes do not contain that string |
1573 |
+ |
|
1574 |
+ |
string zconsOutput(theInfo.finalName); |
1575 |
+ |
|
1576 |
+ |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1577 |
+ |
|
1578 |
+ |
StringData* zconsFilename = new StringData(); |
1579 |
+ |
zconsFilename->setID(ZCONSFILENAME_ID); |
1580 |
+ |
zconsFilename->setData(zconsOutput); |
1581 |
+ |
|
1582 |
+ |
theInfo.addProperty(zconsFilename); |
1583 |
+ |
|
1584 |
+ |
//setup index, pos and other parameters of z-constraint molecules |
1585 |
+ |
nZConstraints = globals->getNzConstraints(); |
1586 |
+ |
theInfo.nZconstraints = nZConstraints; |
1587 |
+ |
|
1588 |
+ |
zconStamp = globals->getZconStamp(); |
1589 |
+ |
ZConsParaItem tempParaItem; |
1590 |
+ |
|
1591 |
+ |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1592 |
+ |
zconsParaData->setID(ZCONSPARADATA_ID); |
1593 |
+ |
|
1594 |
+ |
for (int i = 0; i < nZConstraints; i++){ |
1595 |
+ |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1596 |
+ |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1597 |
+ |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1598 |
+ |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1599 |
+ |
|
1600 |
+ |
zconsParaData->addItem(tempParaItem); |
1601 |
+ |
} |
1602 |
+ |
|
1603 |
+ |
//check the uniqueness of index |
1604 |
+ |
if(!zconsParaData->isIndexUnique()){ |
1605 |
+ |
sprintf(painCave.errMsg, |
1606 |
+ |
"ZConstraint Error: molIndex is not unique\n"); |
1607 |
+ |
painCave.isFatal = 1; |
1608 |
+ |
simError(); |
1609 |
+ |
} |
1610 |
+ |
|
1611 |
+ |
//sort the parameters by index of molecules |
1612 |
+ |
zconsParaData->sortByIndex(); |
1613 |
+ |
|
1614 |
+ |
//push data into siminfo, therefore, we can retrieve later |
1615 |
+ |
theInfo.addProperty(zconsParaData); |
1616 |
+ |
} |