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;
  Component** the_components = NULL;
  LinkedMolStamp* headStamp = NULL;
  LinkedMolStamp* currStamp;

  // 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.haveTauBarostat = 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;

          i++;
          if( i>=argc ){
            sprintf( painCave.errMsg,
                     "\n"
                     "not enough arguments for bilayer\n");
            painCave.isFatal = 0;
            simError();
            usage();
          }       
          strcpy( bsInfo.lipidName, argv[i] );
          
          i++;
          if( i>=argc ){
            sprintf( painCave.errMsg,
                     "\n"
                     "not enough arguments for bilayer\n");
            painCave.isFatal = 0;
            simError();
            usage();
          }       
          strcpy( bsInfo.waterName, argv[i] );

        }

        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;
              strcpy( headInc->name, argv[i] );
            }
            else{ 
              prevInc = headInc;
              currInc = headInc->next;
              while( currInc != NULL ){
                prevInc = currInc;
                currInc = prevInc->next;
              }
              currInc = new includeLinked;
              currInc->next = NULL;
              strcpy( 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( 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",
             bsInfo.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)bsInfo.totNmol / the_globals->getDensity();
    bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
    bsInfo.boxY = bsInfo.boxX;
    bsInfo.boxZ = bsInfo.boxY;
  }
  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 <lipid> <water>  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\n"
                "                                 the lipids randomly oriented in a sea of waters.\n"
                "\n"
                "\n",
                program_name);
  exit(8);
}
Revision:	536
Committed:	Fri May 16 14:28:27 2003 UTC (21 years, 2 months ago) by mmeineke
File size:	12424 byte(s)
Log Message:	doing some work to overhaul sysbuild.
#	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	mmeineke	502	Component** the_components = NULL;
45	mmeineke	501	LinkedMolStamp* headStamp = NULL;
46			LinkedMolStamp* currStamp;
47	mmeineke	495
48	mmeineke	501	// initialize all functions and variables
49	mmeineke	495
50	mmeineke	501	initSimError();
51			program_name = argv[0];
52	mmeineke	495	sysType = -1;
53			have_prefix = 0;
54			isRandom = 0;
55			in_name = NULL;
56	mmeineke	501	headInc = NULL;
57
58			bsInfo.includes = NULL;
59			bsInfo.componentsNmol = NULL;
60			bsInfo.compStamps = NULL;
61			bsInfo.havePressure = 0;
62	mmeineke	502	bsInfo.haveTauBarostat = 0;
63	mmeineke	501	bsInfo.haveTauThermostat = 0;
64			bsInfo.haveQmass = 0;
65
66			headStamp = new LinkedMolStamp();
67			the_stamps = new MakeStamps();
68			the_globals = new Globals();
69			set_interface_stamps( the_stamps, the_globals );
70
71			// parse command line arguments
72
73	mmeineke	495	for( i = 1; i < argc; i++){
74
75			if(argv[i][0] =='-'){
76
77			// parse the option
78
79			if(argv[i][1] == '-' ){
80
81			// parse long word options
82
83			if( !strcmp( argv[i], "--bilayer" ) ){
84			if( sysType > 0 ){
85			sprintf( painCave.errMsg,
86			"You cannot specify more than one system to build.\n" );
87			painCave.isFatal = 0;
88			simError();
89			usage();
90			}
91	mmeineke	536
92	mmeineke	495	sysType = BILAYER;
93	mmeineke	536
94			i++;
95			if( i>=argc ){
96			sprintf( painCave.errMsg,
97			"\n"
98			"not enough arguments for bilayer\n");
99			painCave.isFatal = 0;
100			simError();
101			usage();
102			}
103			strcpy( bsInfo.lipidName, argv[i] );
104
105			i++;
106			if( i>=argc ){
107			sprintf( painCave.errMsg,
108			"\n"
109			"not enough arguments for bilayer\n");
110			painCave.isFatal = 0;
111			simError();
112			usage();
113			}
114			strcpy( bsInfo.waterName, argv[i] );
115
116	mmeineke	495	}
117
118			else{
119			sprintf( painCave.errMsg,
120			"Invalid option \"%s\"\n", argv[i] );
121			painCave.isFatal = 0;
122			simError();
123			usage();
124			}
125			}
126
127			else{
128
129			// parse single character options
130
131			done =0;
132			j = 1;
133			current_flag = argv[i][j];
134			while( (current_flag != '\0') && (!done) ){
135
136			switch(current_flag){
137
138			case 'o':
139			// -o <prefix> => the output prefix.
140
141			i++;
142			out_prefix = argv[i];
143			have_prefix = 1;
144			done = 1;
145			break;
146
147	mmeineke	501	case 'I':
148			// -I <include> => the include file.
149
150			i++;
151			if( headInc == NULL ){
152			headInc = new includeLinked;
153			headInc->next = NULL;
154	mmeineke	502	strcpy( headInc->name, argv[i] );
155	mmeineke	501	}
156			else{
157			prevInc = headInc;
158			currInc = headInc->next;
159			while( currInc != NULL ){
160			prevInc = currInc;
161	mmeineke	502	currInc = prevInc->next;
162	mmeineke	501	}
163			currInc = new includeLinked;
164			currInc->next = NULL;
165	mmeineke	502	strcpy( currInc->name, argv[i] );
166	mmeineke	501	prevInc->next = currInc;
167			}
168
169			done = 1;
170			break;
171
172	mmeineke	495	case 'h':
173			// -h => give the usage
174
175			usage();
176			break;
177
178			case 'r':
179			// toggle random
180
181			isRandom = 1;;
182			break;
183
184			default:
185			sprintf(painCave.errMsg,
186	mmeineke	498	"Bad option \"-%c\"\n", current_flag);
187	mmeineke	495	painCave.isFatal = 0;
188			simError();
189			usage();
190			}
191			j++;
192			current_flag = argv[i][j];
193			}
194			}
195			}
196
197			else{
198
199			if( in_name != NULL ){
200			sprintf( painCave.errMsg,
201			"Error at \"%s\", program does not support\n"
202			"more than one input file.\n"
203			"\n",
204			argv[i]);
205			painCave.isFatal = 0;
206			simError();
207			usage();
208			}
209
210			in_name = argv[i];
211			}
212			}
213
214			if(in_name == NULL){
215	mmeineke	498	sprintf( painCave.errMsg,
216			"No input bass file was specified.\n");
217			painCave.isFatal = 0;
218			simError();
219	mmeineke	495	usage();
220			}
221	mmeineke	498
222			if( sysType < 0 ){
223			sprintf( painCave.errMsg,
224			"No system type was specified.\n");
225			painCave.isFatal = 0;
226			simError();
227			usage();
228			}
229	mmeineke	495
230
231	mmeineke	498	// if no output prefix is given default to "donkey".
232
233			if( !have_prefix ){
234			out_prefix = strdup( "donkey" );
235			}
236	mmeineke	495
237	mmeineke	501	// set command line info into the bassInfo struct
238
239			bsInfo.outPrefix = out_prefix;
240			bsInfo.includes = headInc;
241
242	mmeineke	498
243	mmeineke	501	// open and parse the bass file.
244
245			set_interface_stamps( the_stamps, the_globals );
246	mmeineke	502	yacc_BASS( in_name );
247	mmeineke	501
248			// set the easy ones first
249			bsInfo.targetTemp = the_globals->getTargetTemp();
250			bsInfo.dt = the_globals->getDt();
251			bsInfo.runTime = the_globals->getRunTime();
252
253			// get the ones we know are there, yet still may need some work.
254			bsInfo.nComponents = the_globals->getNComponents();
255			strcpy( bsInfo.forceField, the_globals->getForceField() );
256
257			// get the ensemble:
258			strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
259			if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
260
261			if (the_globals->haveTargetPressure()){
262			bsInfo.targetPressure = the_globals->getTargetPressure();
263			bsInfo.havePressure = 1;
264			}
265			else {
266			sprintf( painCave.errMsg,
267			"sysBuild error: If you use the constant pressure\n"
268			" ensemble, you must set targetPressure.\n"
269			" This was found in the BASS file.\n");
270			painCave.isFatal = 1;
271			simError();
272			}
273
274			if (the_globals->haveTauThermostat()){
275			bsInfo.tauThermostat = the_globals->getTauThermostat();
276			bsInfo.haveTauThermostat = 1;;
277			}
278			else if (the_globals->haveQmass()){
279	mmeineke	502	bsInfo.Qmass = the_globals->getQmass();
280	mmeineke	501	bsInfo.haveQmass = 1;
281			}
282			else {
283			sprintf( painCave.errMsg,
284			"sysBuild error: If you use one of the constant temperature\n"
285			" ensembles, you must set either tauThermostat or qMass.\n"
286			" Neither of these was found in the BASS file.\n");
287			painCave.isFatal = 1;
288			simError();
289			}
290
291			if (the_globals->haveTauBarostat()){
292			bsInfo.tauBarostat = the_globals->getTauBarostat();
293			bsInfo.haveTauBarostat = 1;
294			}
295			else {
296			sprintf( painCave.errMsg,
297			"sysBuild error: If you use the constant pressure\n"
298			" ensemble, you must set tauBarostat.\n"
299			" This was found in the BASS file.\n");
300			painCave.isFatal = 1;
301			simError();
302			}
303
304			}
305			else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
306
307			if (the_globals->haveTauThermostat()){
308			bsInfo.tauThermostat = the_globals->getTauThermostat();
309			bsInfo.haveTauThermostat = 1;
310			}
311			else if (the_globals->haveQmass()){
312			bsInfo.Qmass = the_globals->getQmass();
313			bsInfo.haveQmass = 1;
314			}
315			else {
316			sprintf( painCave.errMsg,
317			"sysBuild error: If you use one of the constant temperature\n"
318			" ensembles, you must set either tauThermostat or qMass.\n"
319			" Neither of these was found in the BASS file.\n");
320			painCave.isFatal = 1;
321			simError();
322			}
323
324			}
325			else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
326
327			// nothing special for now
328			}
329			else {
330			sprintf( painCave.errMsg,
331			"sysBuild Warning. Unrecognized Ensemble -> %s, "
332			"reverting to NVE for this simulation.\n",
333	mmeineke	502	bsInfo.ensemble );
334	mmeineke	501	painCave.isFatal = 0;
335			simError();
336			strcpy( bsInfo.ensemble, "NVE" );
337			}
338
339
340			// get the components and calculate the tot_nMol and indvidual n_mol
341
342			the_components = the_globals->getComponents();
343			bsInfo.componentsNmol = new int[bsInfo.nComponents];
344			bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];
345			bsInfo.totNmol = 0;
346			for( i=0; i<bsInfo.nComponents; i++ ){
347
348			if( !the_components[i]->haveNMol() ){
349			// we have a problem
350			sprintf( painCave.errMsg,
351			"sysBuild Error. No component NMol"
352			" given. Cannot calculate the number of atoms.\n" );
353			painCave.isFatal = 1;
354			simError();
355			}
356
357			bsInfo.totNmol += the_components[i]->getNMol();
358			bsInfo.componentsNmol[i] = the_components[i]->getNMol();
359			}
360
361			// make an array of molecule stamps that match the components used.
362			// also extract the used stamps out into a separate linked list
363
364			for( i=0; i<bsInfo.nComponents; i++ ){
365
366			id = the_components[i]->getType();
367			bsInfo.compStamps[i] = NULL;
368
369			// check to make sure the component isn't already in the list
370
371			bsInfo.compStamps[i] = headStamp->match( id );
372			if( bsInfo.compStamps[i] == NULL ){
373
374			// extract the component from the list;
375
376			currStamp = the_stamps->extractMolStamp( id );
377			if( currStamp == NULL ){
378			sprintf( painCave.errMsg,
379			"sysBuild error: Component \"%s\" was not found in the "
380			"list of declared molecules\n",
381			id );
382			painCave.isFatal = 1;
383			simError();
384			}
385
386			headStamp->add( currStamp );
387			bsInfo.compStamps[i] = headStamp->match( id );
388			}
389			}
390
391			// get and set the boxSize
392
393			if( the_globals->haveBox() ){
394			bsInfo.boxX = the_globals->getBox();
395			bsInfo.boxY = the_globals->getBox();
396	mmeineke	502	bsInfo.boxZ = the_globals->getBox();
397	mmeineke	501	}
398			else if( the_globals->haveDensity() ){
399
400			double vol;
401	mmeineke	502	vol = (double)bsInfo.totNmol / the_globals->getDensity();
402	mmeineke	501	bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
403	mmeineke	502	bsInfo.boxY = bsInfo.boxX;
404			bsInfo.boxZ = bsInfo.boxY;
405	mmeineke	501	}
406			else{
407			if( !the_globals->haveBoxX() ){
408			sprintf( painCave.errMsg,
409			"sysBuild error, no periodic BoxX size given.\n" );
410			painCave.isFatal = 1;
411			simError();
412			}
413			bsInfo.boxX = the_globals->getBoxX();
414
415			if( !the_globals->haveBoxY() ){
416			sprintf( painCave.errMsg,
417			"sysBuild error, no periodic BoxY size given.\n" );
418			painCave.isFatal = 1;
419			simError();
420			}
421			bsInfo.boxY = the_globals->getBoxY();
422
423			if( !the_globals->haveBoxZ() ){
424			sprintf( painCave.errMsg,
425			"SimSetup error, no periodic BoxZ size given.\n" );
426			painCave.isFatal = 1;
427			simError();
428			}
429			bsInfo.boxZ = the_globals->getBoxZ();
430			}
431
432
433			//************************************************************
434			// that should be all we need from bass. now to switch to the
435			// appropriate system builder.
436			// ***********************************************************
437
438
439	mmeineke	498	switch( sysType ){
440
441			case BILAYER:
442
443	mmeineke	501	buildBilayer( isRandom );
444	mmeineke	498	break;
445
446			default:
447			sprintf( painCave.errMsg,
448			"Unknown system type: %d\n", sysType );
449			painCave.isFatal = 1;
450			simError();
451			}
452	mmeineke	495
453	mmeineke	501
454
455			// clean up memory;
456
457			if( headStamp!= NULL ) delete headStamp;
458			if( the_stamps != NULL ) delete the_stamps;
459			if( the_globals != NULL ) delete the_globals;
460			if( the_components != NULL ) delete[] the_components;
461
462			if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
463			if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps;
464			if( bsInfo.includes != NULL ){
465			prevInc = bsInfo.includes;
466			while( prevInc != NULL ){
467			currInc = prevInc->next;
468			delete prevInc;
469			prevInc = currInc;
470			}
471			}
472
473	mmeineke	495	return 0;
474			}
475
476
477			/***************************************************************************
478			* prints out the usage for the command line arguments, then exits.
479			***************************************************************************/
480
481			void usage(){
482			(void)fprintf(stdout,
483			"The proper usage is: %s [options] <input bass>\n"
484			"\n"
485			"Options:\n"
486			"\n"
487			" short:\n"
488			" ------\n"
489			" -h Display this message\n"
490			" -o <prefix> The output prefix\n"
491	mmeineke	501	" -I <include> File name that should be included at the top of the\n"
492			" output bass file.\n"
493	mmeineke	495	" -r toggle the random option\n"
494			"\n"
495			" long:\n"
496			" -----\n"
497	mmeineke	536	" --bilayer <lipid> <water> Tries to build a basic bilayer with the specified number\n"
498			" of lipids in the input bass file. The bilayer will be\n"
499			" surrounded by the number of solvent molecules given\n"
500			" in the bass file.\n"
501			" -note: combined with \"-r\" the simulation will start\n"
502			" the lipids randomly oriented in a sea of waters.\n"
503	mmeineke	495	"\n"
504			"\n",
505			program_name);
506			exit(8);
507			}