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root/group/trunk/OOPSE/utils/sysBuild.cpp
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Comparing trunk/OOPSE/utils/sysBuild.cpp (file contents):
Revision 501 by mmeineke, Tue Apr 15 21:20:35 2003 UTC vs.
Revision 589 by chuckv, Thu Jul 10 19:53:50 2003 UTC

# Line 11 | Line 11
11  
12   #include "sysBuild.hpp"
13   #include "bilayerSys.hpp"
14 + //#include "nanoBuilder.hpp"
15  
16   // this routine is defined in BASS_interface.cpp
17   extern void set_interface_stamps( MakeStamps* ms, Globals* g );
# Line 18 | Line 19 | extern void set_interface_stamps( MakeStamps* ms, Glob
19  
20   // case asignments
21   #define BILAYER 1
22 + #define NANO 2
23  
22 –
24   char* program_name;
25   bassInfo bsInfo;
26   void usage(void);
# Line 41 | Line 42 | int main( int argc, char* argv[]){
42  
43    MakeStamps* the_stamps = NULL;
44    Globals* the_globals = NULL;
45 <  MoleculeStamp** the_components = NULL;
45 >  Component** the_components = NULL;
46    LinkedMolStamp* headStamp = NULL;
47    LinkedMolStamp* currStamp;
48  
48 –  if(
49 –  
49    // initialize all functions and variables
50  
51    initSimError();
# Line 61 | Line 60 | int main( int argc, char* argv[]){
60    bsInfo.componentsNmol = NULL;
61    bsInfo.compStamps = NULL;
62    bsInfo.havePressure = 0;
63 <  bsInfo.haveTauBarrostat = 0;
63 >  bsInfo.haveTauBarostat = 0;
64    bsInfo.haveTauThermostat = 0;
65    bsInfo.haveQmass = 0;
66  
# Line 90 | Line 89 | int main( int argc, char* argv[]){
89              simError();
90              usage();
91            }
92 +
93            sysType = BILAYER;
94 +
95 +          i++;
96 +          if( i>=argc ){
97 +            sprintf( painCave.errMsg,
98 +                     "\n"
99 +                     "not enough arguments for bilayer\n");
100 +            painCave.isFatal = 0;
101 +            simError();
102 +            usage();
103 +          }      
104 +          strcpy( bsInfo.lipidName, argv[i] );
105 +          
106 +          i++;
107 +          if( i>=argc ){
108 +            sprintf( painCave.errMsg,
109 +                     "\n"
110 +                     "not enough arguments for bilayer\n");
111 +            painCave.isFatal = 0;
112 +            simError();
113 +            usage();
114 +          }      
115 +          strcpy( bsInfo.waterName, argv[i] );
116 +
117          }
118  
119          else{
# Line 129 | Line 152 | int main( int argc, char* argv[]){
152              if( headInc == NULL ){
153                headInc = new includeLinked;
154                headInc->next = NULL;
155 <              strcopy( headInc->name, argv[i] );
155 >              strcpy( headInc->name, argv[i] );
156              }
157              else{
158                prevInc = headInc;
159                currInc = headInc->next;
160                while( currInc != NULL ){
161                  prevInc = currInc;
162 <                currInc = previnc->next;
162 >                currInc = prevInc->next;
163                }
164                currInc = new includeLinked;
165                currInc->next = NULL;
166 <              strcopy( currInc->name, argv[i] );
166 >              strcpy( currInc->name, argv[i] );
167                prevInc->next = currInc;
168              }
169              
# Line 221 | Line 244 | int main( int argc, char* argv[]){
244    // open and parse the bass file.
245  
246    set_interface_stamps( the_stamps, the_globals );
247 <  yacc_BASS( info.in_name );  
247 >  yacc_BASS( in_name );  
248  
249    // set the easy ones first
250    bsInfo.targetTemp = the_globals->getTargetTemp();
# Line 254 | Line 277 | int main( int argc, char* argv[]){
277        bsInfo.haveTauThermostat = 1;;
278      }
279      else if (the_globals->haveQmass()){
280 <      bsinfo.Qmass = the_globals->getQmass();
280 >      bsInfo.Qmass = the_globals->getQmass();
281        bsInfo.haveQmass = 1;
282      }
283      else {
# Line 308 | Line 331 | int main( int argc, char* argv[]){
331      sprintf( painCave.errMsg,
332               "sysBuild Warning. Unrecognized Ensemble -> %s, "
333               "reverting to NVE for this simulation.\n",
334 <             ensemble );
334 >             bsInfo.ensemble );
335      painCave.isFatal = 0;
336      simError();
337      strcpy( bsInfo.ensemble, "NVE" );
# Line 371 | Line 394 | int main( int argc, char* argv[]){
394    if( the_globals->haveBox() ){
395      bsInfo.boxX = the_globals->getBox();
396      bsInfo.boxY = the_globals->getBox();
397 <    bsinfo.boxZ = the_globals->getBox();
397 >    bsInfo.boxZ = the_globals->getBox();
398    }
399    else if( the_globals->haveDensity() ){
400  
401      double vol;
402 <    vol = (double)tot_nmol / the_globals->getDensity();
402 >    vol = (double)bsInfo.totNmol / the_globals->getDensity();
403      bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
404 <    bsInfo.boxY = simnfo->box_x;
405 <    bsInfo.boxZ = simnfo->box_x;
404 >    bsInfo.boxY = bsInfo.boxX;
405 >    bsInfo.boxZ = bsInfo.boxY;
406    }
407    else{
408      if( !the_globals->haveBoxX() ){
# Line 419 | Line 442 | int main( int argc, char* argv[]){
442    case BILAYER:
443      
444      buildBilayer( isRandom );
445 +    break;
446 +
447 +  case NANO:
448 +    // buildNano( isRandom );
449      break;
450  
451    default:
# Line 426 | Line 453 | int main( int argc, char* argv[]){
453               "Unknown system type: %d\n", sysType );
454      painCave.isFatal = 1;
455      simError();
456 +
457    }
458    
459  
# Line 472 | Line 500 | void usage(){
500                  "\n"
501                  "  long:\n"
502                  "  -----\n"
503 <                "   --bilayer       Tries to build a basic bilayer with the specified number\n"
504 <                "                     of lipids in the input bass file. The bilayer will be\n"
505 <                "                     surrounded by the number of solvent molecules given\n"
506 <                "                     in the bass file.\n"
507 <                "                      -note: combined with \"-r\" the simulation will start in\n"
508 <                "                             an FCC lattice with randomly assigned latice\n"
481 <                "                             sites for all atoms involved.\n"
503 >                "   --bilayer <lipid> <water>  Tries to build a basic bilayer with the specified number\n"
504 >                "                              of lipids in the input bass file. The bilayer will be\n"
505 >                "                              surrounded by the number of solvent molecules given\n"
506 >                "                              in the bass file.\n"
507 >                "                                -note: combined with \"-r\" the simulation will start\n"
508 >                "                                 the lipids randomly oriented in a sea of waters.\n"
509                  "\n"
510                  "\n",
511                  program_name);

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