OOPSE/utils/sysBuild.cpp

#include <cstdlib>
#include <cstdio>
#include <cstring>
#include <cmath>

#include "simError.h"
#include "parse_me.h"
#include "MakeStamps.hpp"
#include "Globals.hpp"
#include "SimInfo.hpp"

#include "sysBuild.hpp"
#include "bilayerSys.hpp"

// this routine is defined in BASS_interface.cpp
extern void set_interface_stamps( MakeStamps* ms, Globals* g );


// case asignments
#define BILAYER 1


char* program_name;
bassInfo bsInfo;
void usage(void);


int main( int argc, char* argv[]){

  int i,j,k;
  int sysType;
  int done, have_prefix, isRandom;
  char current_flag;
  char* out_prefix;
  char* in_name;
  char* id;
  
  includeLinked* headInc;
  includeLinked* prevInc;
  includeLinked* currInc;

  MakeStamps* the_stamps = NULL;
  Globals* the_globals = NULL;
  MoleculeStamp** the_components = NULL;
  LinkedMolStamp* headStamp = NULL;
  LinkedMolStamp* currStamp;

  if(
  
  // initialize all functions and variables

  initSimError();
  program_name = argv[0];
  sysType = -1;
  have_prefix = 0;
  isRandom = 0;
  in_name = NULL;
  headInc = NULL;

  bsInfo.includes = NULL;
  bsInfo.componentsNmol = NULL;
  bsInfo.compStamps = NULL;
  bsInfo.havePressure = 0;
  bsInfo.haveTauBarrostat = 0;
  bsInfo.haveTauThermostat = 0;
  bsInfo.haveQmass = 0;

  headStamp = new LinkedMolStamp();
  the_stamps = new MakeStamps();
  the_globals = new Globals();
  set_interface_stamps( the_stamps, the_globals );

  // parse command line arguments

  for( i = 1; i < argc; i++){
    
    if(argv[i][0] =='-'){

      // parse the option
      
      if(argv[i][1] == '-' ){

        // parse long word options
        
        if( !strcmp( argv[i], "--bilayer" ) ){
          if( sysType > 0 ){
            sprintf( painCave.errMsg,
                     "You cannot specify more than one system to build.\n" );
            painCave.isFatal = 0;
            simError();
            usage();
          }
          sysType = BILAYER;
        }

        else{
          sprintf( painCave.errMsg,
                   "Invalid option \"%s\"\n", argv[i] );
          painCave.isFatal = 0;
          simError();
          usage();
        }
      }
      
      else{
        
        // parse single character options
        
        done =0;
        j = 1;
        current_flag = argv[i][j];
        while( (current_flag != '\0') && (!done) ){
          
          switch(current_flag){

          case 'o':
            // -o <prefix> => the output prefix.

            i++;
            out_prefix = argv[i];
            have_prefix = 1;
            done = 1;
            break;

          case 'I':
            // -I <include> => the include file.

            i++;
            if( headInc == NULL ){
              headInc = new includeLinked;
              headInc->next = NULL;
              strcopy( headInc->name, argv[i] );
            }
            else{ 
              prevInc = headInc;
              currInc = headInc->next;
              while( currInc != NULL ){
                prevInc = currInc;
                currInc = previnc->next;
              }
              currInc = new includeLinked;
              currInc->next = NULL;
              strcopy( currInc->name, argv[i] );
              prevInc->next = currInc;
            }
             
            done = 1;
            break;

          case 'h':
            // -h => give the usage
            
            usage();
            break;
        
          case 'r':
            // toggle random

            isRandom = 1;;
            break;

          default:
            sprintf(painCave.errMsg, 
                    "Bad option \"-%c\"\n", current_flag);
            painCave.isFatal = 0;
            simError();
            usage();
          }
          j++;
          current_flag = argv[i][j];
        }
      }
    }

    else{
      
      if( in_name != NULL ){
        sprintf( painCave.errMsg, 
                 "Error at \"%s\", program does not support\n"
                 "more than one input file.\n"
                 "\n",
                 argv[i]);
        painCave.isFatal = 0;
        simError();
        usage();
      }

      in_name = argv[i];
    }
  }

  if(in_name == NULL){
    sprintf( painCave.errMsg,
             "No input bass file was specified.\n");
    painCave.isFatal = 0;
    simError();    
    usage();
  }

  if( sysType < 0 ){
    sprintf( painCave.errMsg,
             "No system type was specified.\n");
    painCave.isFatal = 0;
    simError();    
    usage();
  }
  
  
  // if no output prefix is given default to "donkey".

  if( !have_prefix ){
    out_prefix = strdup( "donkey" );
  }
  
  // set command line info into the bassInfo struct
  
  bsInfo.outPrefix = out_prefix;
  bsInfo.includes = headInc;
  

  // open and parse the bass file.

  set_interface_stamps( the_stamps, the_globals );
  yacc_BASS( info.in_name );  

  // set the easy ones first
  bsInfo.targetTemp = the_globals->getTargetTemp();
  bsInfo.dt = the_globals->getDt();
  bsInfo.runTime = the_globals->getRunTime();

  // get the ones we know are there, yet still may need some work.
  bsInfo.nComponents = the_globals->getNComponents();
  strcpy( bsInfo.forceField, the_globals->getForceField() );

  // get the ensemble:
  strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
  if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
    
    if (the_globals->haveTargetPressure()){
      bsInfo.targetPressure = the_globals->getTargetPressure();
      bsInfo.havePressure = 1;
    }
    else {
      sprintf( painCave.errMsg,
               "sysBuild error: If you use the constant pressure\n"
               "    ensemble, you must set targetPressure.\n"
               "    This was found in the BASS file.\n");
      painCave.isFatal = 1;
      simError();
    }

    if (the_globals->haveTauThermostat()){
      bsInfo.tauThermostat = the_globals->getTauThermostat();
      bsInfo.haveTauThermostat = 1;;
    }
    else if (the_globals->haveQmass()){
      bsinfo.Qmass = the_globals->getQmass();
      bsInfo.haveQmass = 1;
    }
    else {
      sprintf( painCave.errMsg,
               "sysBuild error: If you use one of the constant temperature\n"
               "    ensembles, you must set either tauThermostat or qMass.\n"
               "    Neither of these was found in the BASS file.\n");
      painCave.isFatal = 1;
      simError();
    }

    if (the_globals->haveTauBarostat()){
      bsInfo.tauBarostat = the_globals->getTauBarostat();
      bsInfo.haveTauBarostat = 1;
    }                                    
    else {
      sprintf( painCave.errMsg,
               "sysBuild error: If you use the constant pressure\n"
               "    ensemble, you must set tauBarostat.\n"
               "    This was found in the BASS file.\n");
      painCave.isFatal = 1;
      simError();
    }

  } 
  else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {

    if (the_globals->haveTauThermostat()){
      bsInfo.tauThermostat = the_globals->getTauThermostat();
      bsInfo.haveTauThermostat = 1;
    }
    else if (the_globals->haveQmass()){
      bsInfo.Qmass = the_globals->getQmass();
      bsInfo.haveQmass = 1;
    }
    else {
      sprintf( painCave.errMsg,
               "sysBuild error: If you use one of the constant temperature\n"
               "    ensembles, you must set either tauThermostat or qMass.\n"
               "    Neither of these was found in the BASS file.\n");
      painCave.isFatal = 1;
      simError();
    }
    
  } 
  else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
    
    // nothing special for now
  } 
  else {
    sprintf( painCave.errMsg,
             "sysBuild Warning. Unrecognized Ensemble -> %s, "
             "reverting to NVE for this simulation.\n",
             ensemble );
    painCave.isFatal = 0;
    simError();
    strcpy( bsInfo.ensemble, "NVE" );
  }  


  // get the components and calculate the tot_nMol and indvidual n_mol

  the_components = the_globals->getComponents();
  bsInfo.componentsNmol = new int[bsInfo.nComponents];
  bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];  
  bsInfo.totNmol = 0;
  for( i=0; i<bsInfo.nComponents; i++ ){
    
    if( !the_components[i]->haveNMol() ){
      // we have a problem
      sprintf( painCave.errMsg,
               "sysBuild Error. No component NMol"
               " given. Cannot calculate the number of atoms.\n" );
      painCave.isFatal = 1;
      simError();
    }
    
    bsInfo.totNmol += the_components[i]->getNMol();
    bsInfo.componentsNmol[i] = the_components[i]->getNMol();
  }

  // make an array of molecule stamps that match the components used.
  // also extract the used stamps out into a separate linked list
  
  for( i=0; i<bsInfo.nComponents; i++ ){

    id = the_components[i]->getType();
    bsInfo.compStamps[i] = NULL;
    
    // check to make sure the component isn't already in the list

    bsInfo.compStamps[i] = headStamp->match( id );
    if( bsInfo.compStamps[i] == NULL ){
      
      // extract the component from the list;
      
      currStamp = the_stamps->extractMolStamp( id );
      if( currStamp == NULL ){
        sprintf( painCave.errMsg,
                 "sysBuild error: Component \"%s\" was not found in the "
                 "list of declared molecules\n",
                 id );
        painCave.isFatal = 1;
        simError();
      }
      
      headStamp->add( currStamp );
      bsInfo.compStamps[i] = headStamp->match( id );
    }
  }

  // get and set the boxSize

  if( the_globals->haveBox() ){
    bsInfo.boxX = the_globals->getBox();
    bsInfo.boxY = the_globals->getBox();
    bsinfo.boxZ = the_globals->getBox();
  }
  else if( the_globals->haveDensity() ){

    double vol;
    vol = (double)tot_nmol / the_globals->getDensity();
    bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
    bsInfo.boxY = simnfo->box_x;
    bsInfo.boxZ = simnfo->box_x;
  }
  else{
    if( !the_globals->haveBoxX() ){
      sprintf( painCave.errMsg,
               "sysBuild error, no periodic BoxX size given.\n" );
      painCave.isFatal = 1;
      simError();
    }
    bsInfo.boxX = the_globals->getBoxX();

    if( !the_globals->haveBoxY() ){
      sprintf( painCave.errMsg,
               "sysBuild error, no periodic BoxY size given.\n" );
      painCave.isFatal = 1;
      simError();
    }
    bsInfo.boxY = the_globals->getBoxY();

    if( !the_globals->haveBoxZ() ){
      sprintf( painCave.errMsg,
               "SimSetup error, no periodic BoxZ size given.\n" );
      painCave.isFatal = 1;
      simError();
    }
    bsInfo.boxZ = the_globals->getBoxZ();
  }
  

  //************************************************************
  // that should be all we need from bass. now to switch to the
  // appropriate system builder.
  // ***********************************************************


  switch( sysType ){
    
  case BILAYER:
    
    buildBilayer( isRandom );
    break;

  default:
    sprintf( painCave.errMsg,
             "Unknown system type: %d\n", sysType );
    painCave.isFatal = 1;
    simError();
  }
  

  // clean up memory;

  if( headStamp!= NULL )       delete headStamp;
  if( the_stamps != NULL )     delete the_stamps;
  if( the_globals != NULL )    delete the_globals;
  if( the_components != NULL ) delete[] the_components;
  
  if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
  if( bsInfo.compStamps != NULL )     delete[] bsInfo.compStamps;
  if( bsInfo.includes != NULL ){
    prevInc = bsInfo.includes;
    while( prevInc != NULL ){
      currInc = prevInc->next;
      delete prevInc;
      prevInc = currInc;
    }
  }
      
  return 0;
}


/***************************************************************************
 * prints out the usage for the command line arguments, then exits.
 ***************************************************************************/

void usage(){
  (void)fprintf(stdout, 
                "The proper usage is: %s [options] <input bass>\n"
                "\n"
                "Options:\n"
                "\n"
                "  short:\n"
                "  ------\n"
                "   -h              Display this message\n"
                "   -o <prefix>     The output prefix\n"
                "   -I <include>    File name that should be included at the top of the\n"
                "                     output bass file.\n"
                "   -r              toggle the random option\n"
                "\n"
                "  long:\n"
                "  -----\n"
                "   --bilayer       Tries to build a basic bilayer with the specified number\n"
                "                     of lipids in the input bass file. The bilayer will be\n"
                "                     surrounded by the number of solvent molecules given\n"
                "                     in the bass file.\n"
                "                      -note: combined with \"-r\" the simulation will start in\n"
                "                             an FCC lattice with randomly assigned latice\n"
                "                             sites for all atoms involved.\n"
                "\n"
                "\n",
                program_name);
  exit(8);
}
Revision:	501
Committed:	Tue Apr 15 21:20:35 2003 UTC (21 years, 3 months ago) by mmeineke
File size:	11999 byte(s)
Log Message:	finished bilayerSys.cpp sysBuild still need to write the bass file. MoLocator.cpp is currently empty
#	User	Rev	Content
1	mmeineke	495	#include <cstdlib>
2			#include <cstdio>
3			#include <cstring>
4	mmeineke	501	#include <cmath>
5	mmeineke	495
6			#include "simError.h"
7	mmeineke	501	#include "parse_me.h"
8			#include "MakeStamps.hpp"
9			#include "Globals.hpp"
10			#include "SimInfo.hpp"
11	mmeineke	495
12	mmeineke	501	#include "sysBuild.hpp"
13	mmeineke	498	#include "bilayerSys.hpp"
14
15	mmeineke	501	// this routine is defined in BASS_interface.cpp
16			extern void set_interface_stamps( MakeStamps* ms, Globals* g );
17	mmeineke	495
18	mmeineke	501
19			// case asignments
20	mmeineke	495	#define BILAYER 1
21
22
23			char* program_name;
24	mmeineke	501	bassInfo bsInfo;
25	mmeineke	495	void usage(void);
26
27
28			int main( int argc, char* argv[]){
29
30			int i,j,k;
31			int sysType;
32			int done, have_prefix, isRandom;
33			char current_flag;
34			char* out_prefix;
35			char* in_name;
36	mmeineke	501	char* id;
37	mmeineke	498
38	mmeineke	501	includeLinked* headInc;
39			includeLinked* prevInc;
40			includeLinked* currInc;
41	mmeineke	495
42	mmeineke	501	MakeStamps* the_stamps = NULL;
43			Globals* the_globals = NULL;
44			MoleculeStamp** the_components = NULL;
45			LinkedMolStamp* headStamp = NULL;
46			LinkedMolStamp* currStamp;
47	mmeineke	495
48	mmeineke	501	if(
49
50			// initialize all functions and variables
51	mmeineke	495
52	mmeineke	501	initSimError();
53			program_name = argv[0];
54	mmeineke	495	sysType = -1;
55			have_prefix = 0;
56			isRandom = 0;
57			in_name = NULL;
58	mmeineke	501	headInc = NULL;
59
60			bsInfo.includes = NULL;
61			bsInfo.componentsNmol = NULL;
62			bsInfo.compStamps = NULL;
63			bsInfo.havePressure = 0;
64			bsInfo.haveTauBarrostat = 0;
65			bsInfo.haveTauThermostat = 0;
66			bsInfo.haveQmass = 0;
67
68			headStamp = new LinkedMolStamp();
69			the_stamps = new MakeStamps();
70			the_globals = new Globals();
71			set_interface_stamps( the_stamps, the_globals );
72
73			// parse command line arguments
74
75	mmeineke	495	for( i = 1; i < argc; i++){
76
77			if(argv[i][0] =='-'){
78
79			// parse the option
80
81			if(argv[i][1] == '-' ){
82
83			// parse long word options
84
85			if( !strcmp( argv[i], "--bilayer" ) ){
86			if( sysType > 0 ){
87			sprintf( painCave.errMsg,
88			"You cannot specify more than one system to build.\n" );
89			painCave.isFatal = 0;
90			simError();
91			usage();
92			}
93			sysType = BILAYER;
94			}
95
96			else{
97			sprintf( painCave.errMsg,
98			"Invalid option \"%s\"\n", argv[i] );
99			painCave.isFatal = 0;
100			simError();
101			usage();
102			}
103			}
104
105			else{
106
107			// parse single character options
108
109			done =0;
110			j = 1;
111			current_flag = argv[i][j];
112			while( (current_flag != '\0') && (!done) ){
113
114			switch(current_flag){
115
116			case 'o':
117			// -o <prefix> => the output prefix.
118
119			i++;
120			out_prefix = argv[i];
121			have_prefix = 1;
122			done = 1;
123			break;
124
125	mmeineke	501	case 'I':
126			// -I <include> => the include file.
127
128			i++;
129			if( headInc == NULL ){
130			headInc = new includeLinked;
131			headInc->next = NULL;
132			strcopy( headInc->name, argv[i] );
133			}
134			else{
135			prevInc = headInc;
136			currInc = headInc->next;
137			while( currInc != NULL ){
138			prevInc = currInc;
139			currInc = previnc->next;
140			}
141			currInc = new includeLinked;
142			currInc->next = NULL;
143			strcopy( currInc->name, argv[i] );
144			prevInc->next = currInc;
145			}
146
147			done = 1;
148			break;
149
150	mmeineke	495	case 'h':
151			// -h => give the usage
152
153			usage();
154			break;
155
156			case 'r':
157			// toggle random
158
159			isRandom = 1;;
160			break;
161
162			default:
163			sprintf(painCave.errMsg,
164	mmeineke	498	"Bad option \"-%c\"\n", current_flag);
165	mmeineke	495	painCave.isFatal = 0;
166			simError();
167			usage();
168			}
169			j++;
170			current_flag = argv[i][j];
171			}
172			}
173			}
174
175			else{
176
177			if( in_name != NULL ){
178			sprintf( painCave.errMsg,
179			"Error at \"%s\", program does not support\n"
180			"more than one input file.\n"
181			"\n",
182			argv[i]);
183			painCave.isFatal = 0;
184			simError();
185			usage();
186			}
187
188			in_name = argv[i];
189			}
190			}
191
192			if(in_name == NULL){
193	mmeineke	498	sprintf( painCave.errMsg,
194			"No input bass file was specified.\n");
195			painCave.isFatal = 0;
196			simError();
197	mmeineke	495	usage();
198			}
199	mmeineke	498
200			if( sysType < 0 ){
201			sprintf( painCave.errMsg,
202			"No system type was specified.\n");
203			painCave.isFatal = 0;
204			simError();
205			usage();
206			}
207	mmeineke	495
208
209	mmeineke	498	// if no output prefix is given default to "donkey".
210
211			if( !have_prefix ){
212			out_prefix = strdup( "donkey" );
213			}
214	mmeineke	495
215	mmeineke	501	// set command line info into the bassInfo struct
216
217			bsInfo.outPrefix = out_prefix;
218			bsInfo.includes = headInc;
219
220	mmeineke	498
221	mmeineke	501	// open and parse the bass file.
222
223			set_interface_stamps( the_stamps, the_globals );
224			yacc_BASS( info.in_name );
225
226			// set the easy ones first
227			bsInfo.targetTemp = the_globals->getTargetTemp();
228			bsInfo.dt = the_globals->getDt();
229			bsInfo.runTime = the_globals->getRunTime();
230
231			// get the ones we know are there, yet still may need some work.
232			bsInfo.nComponents = the_globals->getNComponents();
233			strcpy( bsInfo.forceField, the_globals->getForceField() );
234
235			// get the ensemble:
236			strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
237			if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
238
239			if (the_globals->haveTargetPressure()){
240			bsInfo.targetPressure = the_globals->getTargetPressure();
241			bsInfo.havePressure = 1;
242			}
243			else {
244			sprintf( painCave.errMsg,
245			"sysBuild error: If you use the constant pressure\n"
246			" ensemble, you must set targetPressure.\n"
247			" This was found in the BASS file.\n");
248			painCave.isFatal = 1;
249			simError();
250			}
251
252			if (the_globals->haveTauThermostat()){
253			bsInfo.tauThermostat = the_globals->getTauThermostat();
254			bsInfo.haveTauThermostat = 1;;
255			}
256			else if (the_globals->haveQmass()){
257			bsinfo.Qmass = the_globals->getQmass();
258			bsInfo.haveQmass = 1;
259			}
260			else {
261			sprintf( painCave.errMsg,
262			"sysBuild error: If you use one of the constant temperature\n"
263			" ensembles, you must set either tauThermostat or qMass.\n"
264			" Neither of these was found in the BASS file.\n");
265			painCave.isFatal = 1;
266			simError();
267			}
268
269			if (the_globals->haveTauBarostat()){
270			bsInfo.tauBarostat = the_globals->getTauBarostat();
271			bsInfo.haveTauBarostat = 1;
272			}
273			else {
274			sprintf( painCave.errMsg,
275			"sysBuild error: If you use the constant pressure\n"
276			" ensemble, you must set tauBarostat.\n"
277			" This was found in the BASS file.\n");
278			painCave.isFatal = 1;
279			simError();
280			}
281
282			}
283			else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
284
285			if (the_globals->haveTauThermostat()){
286			bsInfo.tauThermostat = the_globals->getTauThermostat();
287			bsInfo.haveTauThermostat = 1;
288			}
289			else if (the_globals->haveQmass()){
290			bsInfo.Qmass = the_globals->getQmass();
291			bsInfo.haveQmass = 1;
292			}
293			else {
294			sprintf( painCave.errMsg,
295			"sysBuild error: If you use one of the constant temperature\n"
296			" ensembles, you must set either tauThermostat or qMass.\n"
297			" Neither of these was found in the BASS file.\n");
298			painCave.isFatal = 1;
299			simError();
300			}
301
302			}
303			else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
304
305			// nothing special for now
306			}
307			else {
308			sprintf( painCave.errMsg,
309			"sysBuild Warning. Unrecognized Ensemble -> %s, "
310			"reverting to NVE for this simulation.\n",
311			ensemble );
312			painCave.isFatal = 0;
313			simError();
314			strcpy( bsInfo.ensemble, "NVE" );
315			}
316
317
318			// get the components and calculate the tot_nMol and indvidual n_mol
319
320			the_components = the_globals->getComponents();
321			bsInfo.componentsNmol = new int[bsInfo.nComponents];
322			bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];
323			bsInfo.totNmol = 0;
324			for( i=0; i<bsInfo.nComponents; i++ ){
325
326			if( !the_components[i]->haveNMol() ){
327			// we have a problem
328			sprintf( painCave.errMsg,
329			"sysBuild Error. No component NMol"
330			" given. Cannot calculate the number of atoms.\n" );
331			painCave.isFatal = 1;
332			simError();
333			}
334
335			bsInfo.totNmol += the_components[i]->getNMol();
336			bsInfo.componentsNmol[i] = the_components[i]->getNMol();
337			}
338
339			// make an array of molecule stamps that match the components used.
340			// also extract the used stamps out into a separate linked list
341
342			for( i=0; i<bsInfo.nComponents; i++ ){
343
344			id = the_components[i]->getType();
345			bsInfo.compStamps[i] = NULL;
346
347			// check to make sure the component isn't already in the list
348
349			bsInfo.compStamps[i] = headStamp->match( id );
350			if( bsInfo.compStamps[i] == NULL ){
351
352			// extract the component from the list;
353
354			currStamp = the_stamps->extractMolStamp( id );
355			if( currStamp == NULL ){
356			sprintf( painCave.errMsg,
357			"sysBuild error: Component \"%s\" was not found in the "
358			"list of declared molecules\n",
359			id );
360			painCave.isFatal = 1;
361			simError();
362			}
363
364			headStamp->add( currStamp );
365			bsInfo.compStamps[i] = headStamp->match( id );
366			}
367			}
368
369			// get and set the boxSize
370
371			if( the_globals->haveBox() ){
372			bsInfo.boxX = the_globals->getBox();
373			bsInfo.boxY = the_globals->getBox();
374			bsinfo.boxZ = the_globals->getBox();
375			}
376			else if( the_globals->haveDensity() ){
377
378			double vol;
379			vol = (double)tot_nmol / the_globals->getDensity();
380			bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
381			bsInfo.boxY = simnfo->box_x;
382			bsInfo.boxZ = simnfo->box_x;
383			}
384			else{
385			if( !the_globals->haveBoxX() ){
386			sprintf( painCave.errMsg,
387			"sysBuild error, no periodic BoxX size given.\n" );
388			painCave.isFatal = 1;
389			simError();
390			}
391			bsInfo.boxX = the_globals->getBoxX();
392
393			if( !the_globals->haveBoxY() ){
394			sprintf( painCave.errMsg,
395			"sysBuild error, no periodic BoxY size given.\n" );
396			painCave.isFatal = 1;
397			simError();
398			}
399			bsInfo.boxY = the_globals->getBoxY();
400
401			if( !the_globals->haveBoxZ() ){
402			sprintf( painCave.errMsg,
403			"SimSetup error, no periodic BoxZ size given.\n" );
404			painCave.isFatal = 1;
405			simError();
406			}
407			bsInfo.boxZ = the_globals->getBoxZ();
408			}
409
410
411			//************************************************************
412			// that should be all we need from bass. now to switch to the
413			// appropriate system builder.
414			// ***********************************************************
415
416
417	mmeineke	498	switch( sysType ){
418
419			case BILAYER:
420
421	mmeineke	501	buildBilayer( isRandom );
422	mmeineke	498	break;
423
424			default:
425			sprintf( painCave.errMsg,
426			"Unknown system type: %d\n", sysType );
427			painCave.isFatal = 1;
428			simError();
429			}
430	mmeineke	495
431	mmeineke	501
432
433			// clean up memory;
434
435			if( headStamp!= NULL ) delete headStamp;
436			if( the_stamps != NULL ) delete the_stamps;
437			if( the_globals != NULL ) delete the_globals;
438			if( the_components != NULL ) delete[] the_components;
439
440			if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
441			if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps;
442			if( bsInfo.includes != NULL ){
443			prevInc = bsInfo.includes;
444			while( prevInc != NULL ){
445			currInc = prevInc->next;
446			delete prevInc;
447			prevInc = currInc;
448			}
449			}
450
451	mmeineke	495	return 0;
452			}
453
454
455			/***************************************************************************
456			* prints out the usage for the command line arguments, then exits.
457			***************************************************************************/
458
459			void usage(){
460			(void)fprintf(stdout,
461			"The proper usage is: %s [options] <input bass>\n"
462			"\n"
463			"Options:\n"
464			"\n"
465			" short:\n"
466			" ------\n"
467			" -h Display this message\n"
468			" -o <prefix> The output prefix\n"
469	mmeineke	501	" -I <include> File name that should be included at the top of the\n"
470			" output bass file.\n"
471	mmeineke	495	" -r toggle the random option\n"
472			"\n"
473			" long:\n"
474			" -----\n"
475			" --bilayer Tries to build a basic bilayer with the specified number\n"
476			" of lipids in the input bass file. The bilayer will be\n"
477			" surrounded by the number of solvent molecules given\n"
478			" in the bass file.\n"
479			" -note: combined with \"-r\" the simulation will start in\n"
480			" an FCC lattice with randomly assigned latice\n"
481	mmeineke	498	" sites for all atoms involved.\n"
482	mmeineke	495	"\n"
483			"\n",
484			program_name);
485			exit(8);
486			}