41 |
|
|
42 |
|
MakeStamps* the_stamps = NULL; |
43 |
|
Globals* the_globals = NULL; |
44 |
< |
MoleculeStamp** the_components = NULL; |
44 |
> |
Component** the_components = NULL; |
45 |
|
LinkedMolStamp* headStamp = NULL; |
46 |
|
LinkedMolStamp* currStamp; |
47 |
|
|
48 |
– |
if( |
49 |
– |
|
48 |
|
// initialize all functions and variables |
49 |
|
|
50 |
|
initSimError(); |
59 |
|
bsInfo.componentsNmol = NULL; |
60 |
|
bsInfo.compStamps = NULL; |
61 |
|
bsInfo.havePressure = 0; |
62 |
< |
bsInfo.haveTauBarrostat = 0; |
62 |
> |
bsInfo.haveTauBarostat = 0; |
63 |
|
bsInfo.haveTauThermostat = 0; |
64 |
|
bsInfo.haveQmass = 0; |
65 |
|
|
127 |
|
if( headInc == NULL ){ |
128 |
|
headInc = new includeLinked; |
129 |
|
headInc->next = NULL; |
130 |
< |
strcopy( headInc->name, argv[i] ); |
130 |
> |
strcpy( headInc->name, argv[i] ); |
131 |
|
} |
132 |
|
else{ |
133 |
|
prevInc = headInc; |
134 |
|
currInc = headInc->next; |
135 |
|
while( currInc != NULL ){ |
136 |
|
prevInc = currInc; |
137 |
< |
currInc = previnc->next; |
137 |
> |
currInc = prevInc->next; |
138 |
|
} |
139 |
|
currInc = new includeLinked; |
140 |
|
currInc->next = NULL; |
141 |
< |
strcopy( currInc->name, argv[i] ); |
141 |
> |
strcpy( currInc->name, argv[i] ); |
142 |
|
prevInc->next = currInc; |
143 |
|
} |
144 |
|
|
219 |
|
// open and parse the bass file. |
220 |
|
|
221 |
|
set_interface_stamps( the_stamps, the_globals ); |
222 |
< |
yacc_BASS( info.in_name ); |
222 |
> |
yacc_BASS( in_name ); |
223 |
|
|
224 |
|
// set the easy ones first |
225 |
|
bsInfo.targetTemp = the_globals->getTargetTemp(); |
252 |
|
bsInfo.haveTauThermostat = 1;; |
253 |
|
} |
254 |
|
else if (the_globals->haveQmass()){ |
255 |
< |
bsinfo.Qmass = the_globals->getQmass(); |
255 |
> |
bsInfo.Qmass = the_globals->getQmass(); |
256 |
|
bsInfo.haveQmass = 1; |
257 |
|
} |
258 |
|
else { |
306 |
|
sprintf( painCave.errMsg, |
307 |
|
"sysBuild Warning. Unrecognized Ensemble -> %s, " |
308 |
|
"reverting to NVE for this simulation.\n", |
309 |
< |
ensemble ); |
309 |
> |
bsInfo.ensemble ); |
310 |
|
painCave.isFatal = 0; |
311 |
|
simError(); |
312 |
|
strcpy( bsInfo.ensemble, "NVE" ); |
369 |
|
if( the_globals->haveBox() ){ |
370 |
|
bsInfo.boxX = the_globals->getBox(); |
371 |
|
bsInfo.boxY = the_globals->getBox(); |
372 |
< |
bsinfo.boxZ = the_globals->getBox(); |
372 |
> |
bsInfo.boxZ = the_globals->getBox(); |
373 |
|
} |
374 |
|
else if( the_globals->haveDensity() ){ |
375 |
|
|
376 |
|
double vol; |
377 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
377 |
> |
vol = (double)bsInfo.totNmol / the_globals->getDensity(); |
378 |
|
bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) ); |
379 |
< |
bsInfo.boxY = simnfo->box_x; |
380 |
< |
bsInfo.boxZ = simnfo->box_x; |
379 |
> |
bsInfo.boxY = bsInfo.boxX; |
380 |
> |
bsInfo.boxZ = bsInfo.boxY; |
381 |
|
} |
382 |
|
else{ |
383 |
|
if( !the_globals->haveBoxX() ){ |