87 |
|
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
|
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
|
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 |
< |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
90 |
> |
if (the_globals->haveTargetPressure()) |
91 |
> |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 |
> |
else { |
93 |
> |
sprintf( painCave.errMsg, |
94 |
> |
"SimSetup error: If you use the constant pressure\n" |
95 |
> |
" ensemble, you must set targetPressure.\n" |
96 |
> |
" This was found in the BASS file.\n"); |
97 |
> |
painCave.isFatal = 1; |
98 |
> |
simError(); |
99 |
> |
} |
100 |
> |
|
101 |
> |
if (the_globals->haveTauThermostat()) |
102 |
> |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 |
> |
else if (the_globals->haveQmass()) |
104 |
> |
the_extendedsystem->setQmass(the_globals->getQmass()); |
105 |
> |
else { |
106 |
> |
sprintf( painCave.errMsg, |
107 |
> |
"SimSetup error: If you use one of the constant temperature\n" |
108 |
> |
" ensembles, you must set either tauThermostat or qMass.\n" |
109 |
> |
" Neither of these was found in the BASS file.\n"); |
110 |
> |
painCave.isFatal = 1; |
111 |
> |
simError(); |
112 |
> |
} |
113 |
> |
|
114 |
> |
if (the_globals->haveTauBarostat()) |
115 |
> |
the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 |
> |
else { |
117 |
> |
sprintf( painCave.errMsg, |
118 |
> |
"SimSetup error: If you use the constant pressure\n" |
119 |
> |
" ensemble, you must set tauBarostat.\n" |
120 |
> |
" This was found in the BASS file.\n"); |
121 |
> |
painCave.isFatal = 1; |
122 |
> |
simError(); |
123 |
> |
} |
124 |
> |
|
125 |
|
} else if ( !strcasecmp( ensemble, "NVT") ) { |
126 |
|
the_extendedsystem = new ExtendedSystem( simnfo ); |
127 |
|
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
128 |
+ |
|
129 |
+ |
if (the_globals->haveTauThermostat()) |
130 |
+ |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 |
+ |
else if (the_globals->haveQmass()) |
132 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
133 |
+ |
else { |
134 |
+ |
sprintf( painCave.errMsg, |
135 |
+ |
"SimSetup error: If you use one of the constant temperature\n" |
136 |
+ |
" ensembles, you must set either tauThermostat or qMass.\n" |
137 |
+ |
" Neither of these was found in the BASS file.\n"); |
138 |
+ |
painCave.isFatal = 1; |
139 |
+ |
simError(); |
140 |
+ |
} |
141 |
+ |
|
142 |
|
} else if ( !strcasecmp( ensemble, "NVE") ) { |
143 |
|
} else { |
144 |
|
sprintf( painCave.errMsg, |
154 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 |
|
simnfo->usePBC = the_globals->getPBC(); |
156 |
|
|
157 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
157 |
> |
int usesDipoles = 0; |
158 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 |
> |
the_ff = new TraPPE_ExFF(); |
160 |
> |
usesDipoles = 1; |
161 |
> |
} |
162 |
|
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 |
|
else{ |
164 |
|
sprintf( painCave.errMsg, |
530 |
|
} |
531 |
|
simnfo->dielectric = the_globals->getDielectric(); |
532 |
|
} else { |
533 |
< |
if (simnfo->n_dipoles) { |
533 |
> |
if (usesDipoles) { |
534 |
|
|
535 |
|
if( !the_globals->haveECR() ){ |
536 |
|
sprintf( painCave.errMsg, |
537 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
537 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
538 |
|
"box length for the electrostaticCutoffRadius.\n" |
539 |
|
"I hope you have a very fast processor!\n"); |
540 |
|
painCave.isFatal = 0; |
550 |
|
|
551 |
|
if( !the_globals->haveEST() ){ |
552 |
|
sprintf( painCave.errMsg, |
553 |
< |
"SimSetup Warning: using default value of 5% of the" |
553 |
> |
"SimSetup Warning: using default value of 5%% of the " |
554 |
|
"electrostaticCutoffRadius for the " |
555 |
|
"electrostaticSkinThickness\n" |
556 |
|
); |
725 |
|
|
726 |
|
// new AllLong( simnfo ); |
727 |
|
|
676 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, |
677 |
– |
the_ff, |
678 |
– |
the_extendedsystem); |
679 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, |
680 |
– |
the_ff, |
681 |
– |
the_extendedsystem ); |
728 |
|
|
729 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
730 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
731 |
+ |
std::cerr << "called new Symplecic\n"; |
732 |
+ |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
733 |
+ |
} |
734 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
735 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
736 |
+ |
std::cerr << "called new Verlet\n"; |
737 |
+ |
fprintf( stderr, "called new Verlet. stderr\n" ); |
738 |
+ |
} |
739 |
+ |
else { |
740 |
+ |
std::cerr << "I'm a bug.\n"; |
741 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
742 |
+ |
} |
743 |
|
#ifdef IS_MPI |
744 |
|
mpiSim->mpiRefresh(); |
745 |
|
#endif |