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"
//#include "nanoBuilder.hpp"

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


// case asignments
#define BILAYER 1
#define NANO 2

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;

  case NANO:
    // buildNano( 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:	589
Committed:	Thu Jul 10 19:53:50 2003 UTC (21 years ago) by chuckv
File size:	12523 byte(s)
Log Message:	Added nanoBuilder and a general Lattice builder.
#	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	chuckv	589	//#include "nanoBuilder.hpp"
15	mmeineke	498
16	mmeineke	501	// this routine is defined in BASS_interface.cpp
17			extern void set_interface_stamps( MakeStamps* ms, Globals* g );
18	mmeineke	495
19	mmeineke	501
20			// case asignments
21	mmeineke	495	#define BILAYER 1
22	chuckv	589	#define NANO 2
23	mmeineke	495
24			char* program_name;
25	mmeineke	501	bassInfo bsInfo;
26	mmeineke	495	void usage(void);
27
28
29			int main( int argc, char* argv[]){
30
31			int i,j,k;
32			int sysType;
33			int done, have_prefix, isRandom;
34			char current_flag;
35			char* out_prefix;
36			char* in_name;
37	mmeineke	501	char* id;
38	mmeineke	498
39	mmeineke	501	includeLinked* headInc;
40			includeLinked* prevInc;
41			includeLinked* currInc;
42	mmeineke	495
43	mmeineke	501	MakeStamps* the_stamps = NULL;
44			Globals* the_globals = NULL;
45	mmeineke	502	Component** the_components = NULL;
46	mmeineke	501	LinkedMolStamp* headStamp = NULL;
47			LinkedMolStamp* currStamp;
48	mmeineke	495
49	mmeineke	501	// initialize all functions and variables
50	mmeineke	495
51	mmeineke	501	initSimError();
52			program_name = argv[0];
53	mmeineke	495	sysType = -1;
54			have_prefix = 0;
55			isRandom = 0;
56			in_name = NULL;
57	mmeineke	501	headInc = NULL;
58
59			bsInfo.includes = NULL;
60			bsInfo.componentsNmol = NULL;
61			bsInfo.compStamps = NULL;
62			bsInfo.havePressure = 0;
63	mmeineke	502	bsInfo.haveTauBarostat = 0;
64	mmeineke	501	bsInfo.haveTauThermostat = 0;
65			bsInfo.haveQmass = 0;
66
67			headStamp = new LinkedMolStamp();
68			the_stamps = new MakeStamps();
69			the_globals = new Globals();
70			set_interface_stamps( the_stamps, the_globals );
71
72			// parse command line arguments
73
74	mmeineke	495	for( i = 1; i < argc; i++){
75
76			if(argv[i][0] =='-'){
77
78			// parse the option
79
80			if(argv[i][1] == '-' ){
81
82			// parse long word options
83
84			if( !strcmp( argv[i], "--bilayer" ) ){
85			if( sysType > 0 ){
86			sprintf( painCave.errMsg,
87			"You cannot specify more than one system to build.\n" );
88			painCave.isFatal = 0;
89			simError();
90			usage();
91			}
92	mmeineke	536
93	mmeineke	495	sysType = BILAYER;
94	mmeineke	536
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	mmeineke	495	}
118
119			else{
120			sprintf( painCave.errMsg,
121			"Invalid option \"%s\"\n", argv[i] );
122			painCave.isFatal = 0;
123			simError();
124			usage();
125			}
126			}
127
128			else{
129
130			// parse single character options
131
132			done =0;
133			j = 1;
134			current_flag = argv[i][j];
135			while( (current_flag != '\0') && (!done) ){
136
137			switch(current_flag){
138
139			case 'o':
140			// -o <prefix> => the output prefix.
141
142			i++;
143			out_prefix = argv[i];
144			have_prefix = 1;
145			done = 1;
146			break;
147
148	mmeineke	501	case 'I':
149			// -I <include> => the include file.
150
151			i++;
152			if( headInc == NULL ){
153			headInc = new includeLinked;
154			headInc->next = NULL;
155	mmeineke	502	strcpy( headInc->name, argv[i] );
156	mmeineke	501	}
157			else{
158			prevInc = headInc;
159			currInc = headInc->next;
160			while( currInc != NULL ){
161			prevInc = currInc;
162	mmeineke	502	currInc = prevInc->next;
163	mmeineke	501	}
164			currInc = new includeLinked;
165			currInc->next = NULL;
166	mmeineke	502	strcpy( currInc->name, argv[i] );
167	mmeineke	501	prevInc->next = currInc;
168			}
169
170			done = 1;
171			break;
172
173	mmeineke	495	case 'h':
174			// -h => give the usage
175
176			usage();
177			break;
178
179			case 'r':
180			// toggle random
181
182			isRandom = 1;;
183			break;
184
185			default:
186			sprintf(painCave.errMsg,
187	mmeineke	498	"Bad option \"-%c\"\n", current_flag);
188	mmeineke	495	painCave.isFatal = 0;
189			simError();
190			usage();
191			}
192			j++;
193			current_flag = argv[i][j];
194			}
195			}
196			}
197
198			else{
199
200			if( in_name != NULL ){
201			sprintf( painCave.errMsg,
202			"Error at \"%s\", program does not support\n"
203			"more than one input file.\n"
204			"\n",
205			argv[i]);
206			painCave.isFatal = 0;
207			simError();
208			usage();
209			}
210
211			in_name = argv[i];
212			}
213			}
214
215			if(in_name == NULL){
216	mmeineke	498	sprintf( painCave.errMsg,
217			"No input bass file was specified.\n");
218			painCave.isFatal = 0;
219			simError();
220	mmeineke	495	usage();
221			}
222	mmeineke	498
223			if( sysType < 0 ){
224			sprintf( painCave.errMsg,
225			"No system type was specified.\n");
226			painCave.isFatal = 0;
227			simError();
228			usage();
229			}
230	mmeineke	495
231
232	mmeineke	498	// if no output prefix is given default to "donkey".
233
234			if( !have_prefix ){
235			out_prefix = strdup( "donkey" );
236			}
237	mmeineke	495
238	mmeineke	501	// set command line info into the bassInfo struct
239
240			bsInfo.outPrefix = out_prefix;
241			bsInfo.includes = headInc;
242
243	mmeineke	498
244	mmeineke	501	// open and parse the bass file.
245
246			set_interface_stamps( the_stamps, the_globals );
247	mmeineke	502	yacc_BASS( in_name );
248	mmeineke	501
249			// set the easy ones first
250			bsInfo.targetTemp = the_globals->getTargetTemp();
251			bsInfo.dt = the_globals->getDt();
252			bsInfo.runTime = the_globals->getRunTime();
253
254			// get the ones we know are there, yet still may need some work.
255			bsInfo.nComponents = the_globals->getNComponents();
256			strcpy( bsInfo.forceField, the_globals->getForceField() );
257
258			// get the ensemble:
259			strcpy( bsInfo.ensemble, the_globals->getEnsemble() );
260			if( !strcasecmp( bsInfo.ensemble, "NPT" ) ) {
261
262			if (the_globals->haveTargetPressure()){
263			bsInfo.targetPressure = the_globals->getTargetPressure();
264			bsInfo.havePressure = 1;
265			}
266			else {
267			sprintf( painCave.errMsg,
268			"sysBuild error: If you use the constant pressure\n"
269			" ensemble, you must set targetPressure.\n"
270			" This was found in the BASS file.\n");
271			painCave.isFatal = 1;
272			simError();
273			}
274
275			if (the_globals->haveTauThermostat()){
276			bsInfo.tauThermostat = the_globals->getTauThermostat();
277			bsInfo.haveTauThermostat = 1;;
278			}
279			else if (the_globals->haveQmass()){
280	mmeineke	502	bsInfo.Qmass = the_globals->getQmass();
281	mmeineke	501	bsInfo.haveQmass = 1;
282			}
283			else {
284			sprintf( painCave.errMsg,
285			"sysBuild error: If you use one of the constant temperature\n"
286			" ensembles, you must set either tauThermostat or qMass.\n"
287			" Neither of these was found in the BASS file.\n");
288			painCave.isFatal = 1;
289			simError();
290			}
291
292			if (the_globals->haveTauBarostat()){
293			bsInfo.tauBarostat = the_globals->getTauBarostat();
294			bsInfo.haveTauBarostat = 1;
295			}
296			else {
297			sprintf( painCave.errMsg,
298			"sysBuild error: If you use the constant pressure\n"
299			" ensemble, you must set tauBarostat.\n"
300			" This was found in the BASS file.\n");
301			painCave.isFatal = 1;
302			simError();
303			}
304
305			}
306			else if ( !strcasecmp( bsInfo.ensemble, "NVT") ) {
307
308			if (the_globals->haveTauThermostat()){
309			bsInfo.tauThermostat = the_globals->getTauThermostat();
310			bsInfo.haveTauThermostat = 1;
311			}
312			else if (the_globals->haveQmass()){
313			bsInfo.Qmass = the_globals->getQmass();
314			bsInfo.haveQmass = 1;
315			}
316			else {
317			sprintf( painCave.errMsg,
318			"sysBuild error: If you use one of the constant temperature\n"
319			" ensembles, you must set either tauThermostat or qMass.\n"
320			" Neither of these was found in the BASS file.\n");
321			painCave.isFatal = 1;
322			simError();
323			}
324
325			}
326			else if ( !strcasecmp( bsInfo.ensemble, "NVE") ) {
327
328			// nothing special for now
329			}
330			else {
331			sprintf( painCave.errMsg,
332			"sysBuild Warning. Unrecognized Ensemble -> %s, "
333			"reverting to NVE for this simulation.\n",
334	mmeineke	502	bsInfo.ensemble );
335	mmeineke	501	painCave.isFatal = 0;
336			simError();
337			strcpy( bsInfo.ensemble, "NVE" );
338			}
339
340
341			// get the components and calculate the tot_nMol and indvidual n_mol
342
343			the_components = the_globals->getComponents();
344			bsInfo.componentsNmol = new int[bsInfo.nComponents];
345			bsInfo.compStamps = new MoleculeStamp*[bsInfo.nComponents];
346			bsInfo.totNmol = 0;
347			for( i=0; i<bsInfo.nComponents; i++ ){
348
349			if( !the_components[i]->haveNMol() ){
350			// we have a problem
351			sprintf( painCave.errMsg,
352			"sysBuild Error. No component NMol"
353			" given. Cannot calculate the number of atoms.\n" );
354			painCave.isFatal = 1;
355			simError();
356			}
357
358			bsInfo.totNmol += the_components[i]->getNMol();
359			bsInfo.componentsNmol[i] = the_components[i]->getNMol();
360			}
361
362			// make an array of molecule stamps that match the components used.
363			// also extract the used stamps out into a separate linked list
364
365			for( i=0; i<bsInfo.nComponents; i++ ){
366
367			id = the_components[i]->getType();
368			bsInfo.compStamps[i] = NULL;
369
370			// check to make sure the component isn't already in the list
371
372			bsInfo.compStamps[i] = headStamp->match( id );
373			if( bsInfo.compStamps[i] == NULL ){
374
375			// extract the component from the list;
376
377			currStamp = the_stamps->extractMolStamp( id );
378			if( currStamp == NULL ){
379			sprintf( painCave.errMsg,
380			"sysBuild error: Component \"%s\" was not found in the "
381			"list of declared molecules\n",
382			id );
383			painCave.isFatal = 1;
384			simError();
385			}
386
387			headStamp->add( currStamp );
388			bsInfo.compStamps[i] = headStamp->match( id );
389			}
390			}
391
392			// get and set the boxSize
393
394			if( the_globals->haveBox() ){
395			bsInfo.boxX = the_globals->getBox();
396			bsInfo.boxY = the_globals->getBox();
397	mmeineke	502	bsInfo.boxZ = the_globals->getBox();
398	mmeineke	501	}
399			else if( the_globals->haveDensity() ){
400
401			double vol;
402	mmeineke	502	vol = (double)bsInfo.totNmol / the_globals->getDensity();
403	mmeineke	501	bsInfo.boxX = pow( vol, ( 1.0 / 3.0 ) );
404	mmeineke	502	bsInfo.boxY = bsInfo.boxX;
405			bsInfo.boxZ = bsInfo.boxY;
406	mmeineke	501	}
407			else{
408			if( !the_globals->haveBoxX() ){
409			sprintf( painCave.errMsg,
410			"sysBuild error, no periodic BoxX size given.\n" );
411			painCave.isFatal = 1;
412			simError();
413			}
414			bsInfo.boxX = the_globals->getBoxX();
415
416			if( !the_globals->haveBoxY() ){
417			sprintf( painCave.errMsg,
418			"sysBuild error, no periodic BoxY size given.\n" );
419			painCave.isFatal = 1;
420			simError();
421			}
422			bsInfo.boxY = the_globals->getBoxY();
423
424			if( !the_globals->haveBoxZ() ){
425			sprintf( painCave.errMsg,
426			"SimSetup error, no periodic BoxZ size given.\n" );
427			painCave.isFatal = 1;
428			simError();
429			}
430			bsInfo.boxZ = the_globals->getBoxZ();
431			}
432
433
434			//************************************************************
435			// that should be all we need from bass. now to switch to the
436			// appropriate system builder.
437			// ***********************************************************
438
439
440	mmeineke	498	switch( sysType ){
441
442			case BILAYER:
443
444	mmeineke	501	buildBilayer( isRandom );
445	mmeineke	498	break;
446
447	chuckv	589	case NANO:
448			// buildNano( isRandom );
449			break;
450
451	mmeineke	498	default:
452			sprintf( painCave.errMsg,
453			"Unknown system type: %d\n", sysType );
454			painCave.isFatal = 1;
455			simError();
456	chuckv	589
457	mmeineke	498	}
458	mmeineke	495
459	mmeineke	501
460
461			// clean up memory;
462
463			if( headStamp!= NULL ) delete headStamp;
464			if( the_stamps != NULL ) delete the_stamps;
465			if( the_globals != NULL ) delete the_globals;
466			if( the_components != NULL ) delete[] the_components;
467
468			if( bsInfo.componentsNmol != NULL ) delete[] bsInfo.componentsNmol;
469			if( bsInfo.compStamps != NULL ) delete[] bsInfo.compStamps;
470			if( bsInfo.includes != NULL ){
471			prevInc = bsInfo.includes;
472			while( prevInc != NULL ){
473			currInc = prevInc->next;
474			delete prevInc;
475			prevInc = currInc;
476			}
477			}
478
479	mmeineke	495	return 0;
480			}
481
482
483			/***************************************************************************
484			* prints out the usage for the command line arguments, then exits.
485			***************************************************************************/
486
487			void usage(){
488			(void)fprintf(stdout,
489			"The proper usage is: %s [options] <input bass>\n"
490			"\n"
491			"Options:\n"
492			"\n"
493			" short:\n"
494			" ------\n"
495			" -h Display this message\n"
496			" -o <prefix> The output prefix\n"
497	mmeineke	501	" -I <include> File name that should be included at the top of the\n"
498			" output bass file.\n"
499	mmeineke	495	" -r toggle the random option\n"
500			"\n"
501			" long:\n"
502			" -----\n"
503	mmeineke	536	" --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	mmeineke	495	"\n"
510			"\n",
511			program_name);
512			exit(8);
513			}