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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 614 by mmeineke, Tue Jul 15 17:57:04 2003 UTC vs.
Revision 1104 by gezelter, Tue Apr 13 16:26:03 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 41 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
83	–	int i, j, k, globalAtomIndex;
84	–
126		// gather all of the information from the Bass file
127	<
127	>
128		gatherInfo();
129
130		// creation of complex system objects
131
132		sysObjectsCreation();
133
93	–
94	–
95	–	// initialize the arrays
96	–
97	–
98	–
99	–	makeMolecules();
100	–	info->identArray = new int[info->n_atoms];
101	–	for(i=0; i<info->n_atoms; i++){
102	–	info->identArray[i] = the_atoms[i]->getIdent();
103	–	}
104	–
105	–
134		// check on the post processing info
135	<
135	>
136		finalInfoCheck();
137
110	–
111	–
112	–
138		// initialize the system coordinates
139
140	<	initSystemCoords();
141	<
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	+	if( !(globals->getUseInitTime()) )
144	+	info[0].currentTime = 0.0;
145	+	}
146	+
147		// make the output filenames
148
149		makeOutNames();
121	–
122	–
123	–
150
151	+	if (globals->haveMinimizer())
152	+	// make minimizer
153	+	makeMinimizer();
154	+	else
155	+	// make the integrator
156	+	makeIntegrator();
157
126	–
127	–
128	–
129	–
130	–	// make the integrator
131	–
132	–
133	–	NVT*  myNVT = NULL;
134	–	NPTi* myNPTi = NULL;
135	–	NPTf* myNPTf = NULL;
136	–	NPTim* myNPTim = NULL;
137	–	NPTfm* myNPTfm = NULL;
138	–
139	–	switch( ensembleCase ){
140	–
141	–	case NVE_ENS:
142	–	new NVE( info, the_ff );
143	–	break;
144	–
145	–	case NVT_ENS:
146	–	myNVT = new NVT( info, the_ff );
147	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
148	–
149	–	if (the_globals->haveTauThermostat())
150	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
151	–
152	–	else {
153	–	sprintf( painCave.errMsg,
154	–	"SimSetup error: If you use the NVT\n"
155	–	"    ensemble, you must set tauThermostat.\n");
156	–	painCave.isFatal = 1;
157	–	simError();
158	–	}
159	–	break;
160	–
161	–	case NPTi_ENS:
162	–	myNPTi = new NPTi( info, the_ff );
163	–	myNPTi->setTargetTemp( the_globals->getTargetTemp() );
164	–
165	–	if (the_globals->haveTargetPressure())
166	–	myNPTi->setTargetPressure(the_globals->getTargetPressure());
167	–	else {
168	–	sprintf( painCave.errMsg,
169	–	"SimSetup error: If you use a constant pressure\n"
170	–	"    ensemble, you must set targetPressure in the BASS file.\n");
171	–	painCave.isFatal = 1;
172	–	simError();
173	–	}
174	–
175	–	if( the_globals->haveTauThermostat() )
176	–	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
177	–	else{
178	–	sprintf( painCave.errMsg,
179	–	"SimSetup error: If you use an NPT\n"
180	–	"    ensemble, you must set tauThermostat.\n");
181	–	painCave.isFatal = 1;
182	–	simError();
183	–	}
184	–
185	–	if( the_globals->haveTauBarostat() )
186	–	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
187	–	else{
188	–	sprintf( painCave.errMsg,
189	–	"SimSetup error: If you use an NPT\n"
190	–	"    ensemble, you must set tauBarostat.\n");
191	–	painCave.isFatal = 1;
192	–	simError();
193	–	}
194	–	break;
195	–
196	–	case NPTf_ENS:
197	–	myNPTf = new NPTf( info, the_ff );
198	–	myNPTf->setTargetTemp( the_globals->getTargetTemp());
199	–
200	–	if (the_globals->haveTargetPressure())
201	–	myNPTf->setTargetPressure(the_globals->getTargetPressure());
202	–	else {
203	–	sprintf( painCave.errMsg,
204	–	"SimSetup error: If you use a constant pressure\n"
205	–	"    ensemble, you must set targetPressure in the BASS file.\n");
206	–	painCave.isFatal = 1;
207	–	simError();
208	–	}
209	–
210	–	if( the_globals->haveTauThermostat() )
211	–	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
212	–	else{
213	–	sprintf( painCave.errMsg,
214	–	"SimSetup error: If you use an NPT\n"
215	–	"    ensemble, you must set tauThermostat.\n");
216	–	painCave.isFatal = 1;
217	–	simError();
218	–	}
219	–
220	–	if( the_globals->haveTauBarostat() )
221	–	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
222	–	else{
223	–	sprintf( painCave.errMsg,
224	–	"SimSetup error: If you use an NPT\n"
225	–	"    ensemble, you must set tauBarostat.\n");
226	–	painCave.isFatal = 1;
227	–	simError();
228	–	}
229	–	break;
230	–
231	–	case NPTim_ENS:
232	–	myNPTim = new NPTim( info, the_ff );
233	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
234	–
235	–	if (the_globals->haveTargetPressure())
236	–	myNPTim->setTargetPressure(the_globals->getTargetPressure());
237	–	else {
238	–	sprintf( painCave.errMsg,
239	–	"SimSetup error: If you use a constant pressure\n"
240	–	"    ensemble, you must set targetPressure in the BASS file.\n");
241	–	painCave.isFatal = 1;
242	–	simError();
243	–	}
244	–
245	–	if( the_globals->haveTauThermostat() )
246	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
247	–	else{
248	–	sprintf( painCave.errMsg,
249	–	"SimSetup error: If you use an NPT\n"
250	–	"    ensemble, you must set tauThermostat.\n");
251	–	painCave.isFatal = 1;
252	–	simError();
253	–	}
254	–
255	–	if( the_globals->haveTauBarostat() )
256	–	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
257	–	else{
258	–	sprintf( painCave.errMsg,
259	–	"SimSetup error: If you use an NPT\n"
260	–	"    ensemble, you must set tauBarostat.\n");
261	–	painCave.isFatal = 1;
262	–	simError();
263	–	}
264	–	break;
265	–
266	–	case NPTfm_ENS:
267	–	myNPTfm = new NPTfm( info, the_ff );
268	–	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
269	–
270	–	if (the_globals->haveTargetPressure())
271	–	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
272	–	else {
273	–	sprintf( painCave.errMsg,
274	–	"SimSetup error: If you use a constant pressure\n"
275	–	"    ensemble, you must set targetPressure in the BASS file.\n");
276	–	painCave.isFatal = 1;
277	–	simError();
278	–	}
279	–
280	–	if( the_globals->haveTauThermostat() )
281	–	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
282	–	else{
283	–	sprintf( painCave.errMsg,
284	–	"SimSetup error: If you use an NPT\n"
285	–	"    ensemble, you must set tauThermostat.\n");
286	–	painCave.isFatal = 1;
287	–	simError();
288	–	}
289	–
290	–	if( the_globals->haveTauBarostat() )
291	–	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
292	–	else{
293	–	sprintf( painCave.errMsg,
294	–	"SimSetup error: If you use an NPT\n"
295	–	"    ensemble, you must set tauBarostat.\n");
296	–	painCave.isFatal = 1;
297	–	simError();
298	–	}
299	–	break;
300	–
301	–	default:
302	–	sprintf( painCave.errMsg,
303	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
304	–	painCave.isFatal = 1;
305	–	simError();
306	–	}
307	–
308	–
158		#ifdef IS_MPI
159		mpiSim->mpiRefresh();
160		#endif
161
162		// initialize the Fortran
163
164	<
316	<	info->refreshSim();
317	<
318	<	if( !strcmp( info->mixingRule, "standard") ){
319	<	the_ff->initForceField( LB_MIXING_RULE );
320	<	}
321	<	else if( !strcmp( info->mixingRule, "explicit") ){
322	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
323	<	}
324	<	else{
325	<	sprintf( painCave.errMsg,
326	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
327	<	info->mixingRule );
328	<	painCave.isFatal = 1;
329	<	simError();
330	<	}
331	<
332	<
333	<	#ifdef IS_MPI
334	<	strcpy( checkPointMsg,
335	<	"Successfully intialized the mixingRule for Fortran." );
336	<	MPIcheckPoint();
337	<	#endif // is_mpi
164	>	initFortran();
165		}
166
167
168	<	void SimSetup::makeMolecules( void ){
169	<
170	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
171	<	molInit info;
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174	>	molInit molInfo;
175		DirectionalAtom* dAtom;
176	+	RigidBody* myRB;
177	+	StuntDouble* mySD;
178		LinkedAssign* extras;
179		LinkedAssign* current_extra;
180		AtomStamp* currentAtom;
181		BondStamp* currentBond;
182		BendStamp* currentBend;
183		TorsionStamp* currentTorsion;
184	+	RigidBodyStamp* currentRigidBody;
185
186		bond_pair* theBonds;
187		bend_set* theBends;
188		torsion_set* theTorsions;
189
190	<
190	>	set<int> skipList;
191	>
192	>	double phi, theta, psi;
193	>
194		//init the forceField paramters
195
196		the_ff->readParams();
197
362	–
198		// init the atoms
199
200	<	double ux, uy, uz, u, uSqr;
366	<
367	<	atomOffset = 0;
368	<	excludeOffset = 0;
369	<	for(i=0; i<info->n_mol; i++){
370	<
371	<	stampID = the_molecules[i].getStampID();
200	>	int nMembers, nNew, rb1, rb2;
201
202	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
203	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
375	<	info.nBends    = comp_stamps[stampID]->getNBends();
376	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
377	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
202	>	for (k = 0; k < nInfo; k++){
203	>	the_ff->setSimInfo(&(info[k]));
204
205	<	info.myAtoms = &the_atoms[atomOffset];
380	<	info.myExcludes = &the_excludes[excludeOffset];
381	<	info.myBonds = new Bond*[info.nBonds];
382	<	info.myBends = new Bend*[info.nBends];
383	<	info.myTorsions = new Torsion*[info.nTorsions];
205	>	atomOffset = 0;
206
207	<	theBonds = new bond_pair[info.nBonds];
208	<	theBends = new bend_set[info.nBends];
209	<	theTorsions = new torsion_set[info.nTorsions];
210	<
211	<	// make the Atoms
212	<
213	<	for(j=0; j<info.nAtoms; j++){
207	>	for (i = 0; i < info[k].n_mol; i++){
208	>	stampID = info[k].molecules[i].getStampID();
209	>
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215
216	<	currentAtom = comp_stamps[stampID]->getAtom( j );
217	<	if( currentAtom->haveOrientation() ){
218	<
219	<	dAtom = new DirectionalAtom(j + atomOffset);
220	<	info->n_oriented++;
221	<	info.myAtoms[j] = dAtom;
222	<
223	<	ux = currentAtom->getOrntX();
224	<	uy = currentAtom->getOrntY();
225	<	uz = currentAtom->getOrntZ();
226	<
227	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
228	<
229	<	u = sqrt( uSqr );
230	<	ux = ux / u;
231	<	uy = uy / u;
232	<	uz = uz / u;
233	<
234	<	dAtom->setSUx( ux );
235	<	dAtom->setSUy( uy );
236	<	dAtom->setSUz( uz );
216	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
217	>
218	>	if (molInfo.nBonds > 0)
219	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	>	else
221	>	molInfo.myBonds = NULL;
222	>
223	>	if (molInfo.nBends > 0)
224	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	>	else
226	>	molInfo.myBends = NULL;
227	>
228	>	if (molInfo.nTorsions > 0)
229	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	>	else
231	>	molInfo.myTorsions = NULL;
232	>
233	>	theBonds = new bond_pair[molInfo.nBonds];
234	>	theBends = new bend_set[molInfo.nBends];
235	>	theTorsions = new torsion_set[molInfo.nTorsions];
236	>
237	>	// make the Atoms
238	>
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241	>
242	>	if (currentAtom->haveOrientation()){
243	>	dAtom = new DirectionalAtom((j + atomOffset),
244	>	info[k].getConfiguration());
245	>	info[k].n_oriented++;
246	>	molInfo.myAtoms[j] = dAtom;
247	>
248	>	// Directional Atoms have standard unit vectors which are oriented
249	>	// in space using the three Euler angles.  We assume the standard
250	>	// unit vector was originally along the z axis below.
251	>
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255	>
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260	>
261	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	>	}
263	>
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265	>
266	>	#ifdef IS_MPI
267	>
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269	>
270	>	#endif // is_mpi
271	>	}
272	>
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278	>
279	>	tempI = theBonds[j].a;
280	>	tempJ = theBonds[j].b;
281	>
282	>	#ifdef IS_MPI
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289	>
290	>	info[k].excludes->addPair(exI, exJ);
291		}
292	<	else{
293	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
294	<	}
295	<	info.myAtoms[j]->setType( currentAtom->getType() );
296	<
292	>
293	>	//make the bends
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299	>
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303	>
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311	>
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317	>
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336	>
337	>	current_extra = current_extra->getNext();
338	>	}
339	>	}
340	>
341	>	if (theBends[j].isGhost) {
342	>
343	>	tempI = theBends[j].a;
344	>	tempJ = theBends[j].b;
345	>
346		#ifdef IS_MPI
347	<
348	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
349	<
350	<	#endif // is_mpi
351	<	}
352	<
353	<	// make the bonds
428	<	for(j=0; j<info.nBonds; j++){
429	<
430	<	currentBond = comp_stamps[stampID]->getBond( j );
431	<	theBonds[j].a = currentBond->getA() + atomOffset;
432	<	theBonds[j].b = currentBond->getB() + atomOffset;
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354
355	<	exI = theBonds[j].a;
435	<	exJ = theBonds[j].b;
355	>	} else {
356
357	<	// exclude_I must always be the smaller of the pair
358	<	if( exI > exJ ){
359	<	tempEx = exI;
360	<	exI = exJ;
441	<	exJ = tempEx;
442	<	}
357	>	tempI = theBends[j].a;
358	>	tempJ = theBends[j].b;
359	>	tempK = theBends[j].c;
360	>
361		#ifdef IS_MPI
362	<	tempEx = exI;
363	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
364	<	tempEx = exJ;
365	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
366	<
367	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
368	<	#else  // isn't MPI
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375	>	}
376
377	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	<	#endif  //is_mpi
379	<	}
380	<	excludeOffset += info.nBonds;
377	>	for (j = 0; j < molInfo.nTorsions; j++){
378	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383
384	<	//make the bends
385	<	for(j=0; j<info.nBends; j++){
386	<
387	<	currentBend = comp_stamps[stampID]->getBend( j );
388	<	theBends[j].a = currentBend->getA() + atomOffset;
462	<	theBends[j].b = currentBend->getB() + atomOffset;
463	<	theBends[j].c = currentBend->getC() + atomOffset;
464	<
465	<	if( currentBend->haveExtras() ){
466	<
467	<	extras = currentBend->getExtras();
468	<	current_extra = extras;
469	<
470	<	while( current_extra != NULL ){
471	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
472	<
473	<	switch( current_extra->getType() ){
474	<
475	<	case 0:
476	<	theBends[j].ghost =
477	<	current_extra->getInt() + atomOffset;
478	<	theBends[j].isGhost = 1;
479	<	break;
480	<
481	<	case 1:
482	<	theBends[j].ghost =
483	<	(int)current_extra->getDouble() + atomOffset;
484	<	theBends[j].isGhost = 1;
485	<	break;
486	<
487	<	default:
488	<	sprintf( painCave.errMsg,
489	<	"SimSetup Error: ghostVectorSource was neither a "
490	<	"double nor an int.\n"
491	<	"-->Bend[%d] in %s\n",
492	<	j, comp_stamps[stampID]->getID() );
493	<	painCave.isFatal = 1;
494	<	simError();
495	<	}
496	<	}
497	<
498	<	else{
499	<
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Error: unhandled bend assignment:\n"
502	<	"    -->%s in Bend[%d] in %s\n",
503	<	current_extra->getlhs(),
504	<	j, comp_stamps[stampID]->getID() );
505	<	painCave.isFatal = 1;
506	<	simError();
507	<	}
508	<
509	<	current_extra = current_extra->getNext();
510	<	}
511	<	}
512	<
513	<	if( !theBends[j].isGhost ){
514	<
515	<	exI = theBends[j].a;
516	<	exJ = theBends[j].c;
517	<	}
518	<	else{
519	<
520	<	exI = theBends[j].a;
521	<	exJ = theBends[j].b;
522	<	}
523	<
524	<	// exclude_I must always be the smaller of the pair
525	<	if( exI > exJ ){
526	<	tempEx = exI;
527	<	exI = exJ;
528	<	exJ = tempEx;
529	<	}
384	>	tempI = theTorsions[j].a;
385	>	tempJ = theTorsions[j].b;
386	>	tempK = theTorsions[j].c;
387	>	tempL = theTorsions[j].d;
388	>
389		#ifdef IS_MPI
390	<	tempEx = exI;
391	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
392	<	tempEx = exJ;
393	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
394	<
395	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
396	<	#else  // isn't MPI
397	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
398	<	#endif  //is_mpi
399	<	}
541	<	excludeOffset += info.nBends;
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399	>	#endif
400
401	<	for(j=0; j<info.nTorsions; j++){
402	<
403	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
404	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
405	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
406	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
549	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
550	<
551	<	exI = theTorsions[j].a;
552	<	exJ = theTorsions[j].d;
553	<
554	<	// exclude_I must always be the smaller of the pair
555	<	if( exI > exJ ){
556	<	tempEx = exI;
557	<	exI = exJ;
558	<	exJ = tempEx;
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407		}
560	–	#ifdef IS_MPI
561	–	tempEx = exI;
562	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
563	–	tempEx = exJ;
564	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
565	–
566	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
567	–	#else  // isn't MPI
568	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
569	–	#endif  //is_mpi
570	–	}
571	–	excludeOffset += info.nTorsions;
408
409	<
574	<	// send the arrays off to the forceField for init.
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410
411	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
412	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
578	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
411	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	>	nMembers = currentRigidBody->getNMembers();
413
414	+	// Create the Rigid Body:
415
416	<	the_molecules[i].initialize( info );
416	>	myRB = new RigidBody();
417	>
418	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
419
420	+	// molI is atom numbering inside this molecule
421	+	molI = currentRigidBody->getMember(rb1);
422
423	<	atomOffset += info.nAtoms;
424	<	delete[] theBonds;
425	<	delete[] theBends;
426	<	delete[] theTorsions;
423	>	// tempI is atom numbering on local processor
424	>	tempI = molI + atomOffset;
425	>
426	>	// currentAtom is the AtomStamp (which we need for
427	>	// rigid body reference positions)
428	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
429	>
430	>	// When we add to the rigid body, add the atom itself and
431	>	// the stamp info:
432	>
433	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	>
435	>	// Add this atom to the Skip List for the integrators
436	>	#ifdef IS_MPI
437	>	slI = info[k].atoms[tempI]->getGlobalIndex();
438	>	#else
439	>	slI = tempI;
440	>	#endif
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468	>
469	>	molInfo.myRigidBodies.push_back(myRB);
470	>	info[k].rigidBodies.push_back(myRB);
471	>	}
472	>
473	>
474	>	// After this is all set up, scan through the atoms to
475	>	// see if they can be added to the integrableObjects:
476	>
477	>	for (j = 0; j < molInfo.nAtoms; j++){
478	>
479	>	#ifdef IS_MPI
480	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
481	>	#else
482	>	slJ = j+atomOffset;
483	>	#endif
484	>
485	>	// if they aren't on the skip list, then they can be integrated
486	>
487	>	if (skipList.find(slJ) == skipList.end()) {
488	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
489	>	info[k].integrableObjects.push_back(mySD);
490	>	molInfo.myIntegrableObjects.push_back(mySD);
491	>	}
492	>	}
493	>
494	>	// all rigid bodies are integrated:
495	>
496	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
497	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
498	>	info[k].integrableObjects.push_back(mySD);
499	>	molInfo.myIntegrableObjects.push_back(mySD);
500	>	}
501	>
502	>
503	>	// send the arrays off to the forceField for init.
504	>
505	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
506	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
507	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
508	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
509	>	theTorsions);
510	>
511	>	info[k].molecules[i].initialize(molInfo);
512	>
513	>
514	>	atomOffset += molInfo.nAtoms;
515	>	delete[] theBonds;
516	>	delete[] theBends;
517	>	delete[] theTorsions;
518	>	}
519		}
520
521		#ifdef IS_MPI
522	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
522	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
523		MPIcheckPoint();
524		#endif // is_mpi
525
526		// clean up the forcefield
597	–	the_ff->calcRcut();
598	–	the_ff->cleanMe();
527
528	<	}
528	>	if (!globals->haveLJrcut()){
529
530	<	void SimSetup::initFromBass( void ){
530	>	the_ff->calcRcut();
531
532	+	} else {
533	+
534	+	the_ff->setRcut( globals->getLJrcut() );
535	+	}
536	+
537	+	the_ff->cleanMe();
538	+	}
539	+
540	+	void SimSetup::initFromBass(void){
541		int i, j, k;
542		int n_cells;
543		double cellx, celly, cellz;
#	Line 609 | Line 546 | void SimSetup::initFromBass( void ){
546		int n_extra;
547		int have_extra, done;
548
549	<	temp1 = (double)tot_nmol / 4.0;
550	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
551	<	temp3 = ceil( temp2 );
549	>	double vel[3];
550	>	vel[0] = 0.0;
551	>	vel[1] = 0.0;
552	>	vel[2] = 0.0;
553
554	<	have_extra =0;
555	<	if( temp2 < temp3 ){ // we have a non-complete lattice
556	<	have_extra =1;
554	>	temp1 = (double) tot_nmol / 4.0;
555	>	temp2 = pow(temp1, (1.0 / 3.0));
556	>	temp3 = ceil(temp2);
557
558	<	n_cells = (int)temp3 - 1;
559	<	cellx = info->boxLx / temp3;
560	<	celly = info->boxLy / temp3;
561	<	cellz = info->boxLz / temp3;
624	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
625	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
626	<	n_per_extra = (int)ceil( temp1 );
558	>	have_extra = 0;
559	>	if (temp2 < temp3){
560	>	// we have a non-complete lattice
561	>	have_extra = 1;
562
563	<	if( n_per_extra > 4){
564	<	sprintf( painCave.errMsg,
565	<	"SimSetup error. There has been an error in constructing"
566	<	" the non-complete lattice.\n" );
563	>	n_cells = (int) temp3 - 1;
564	>	cellx = info[0].boxL[0] / temp3;
565	>	celly = info[0].boxL[1] / temp3;
566	>	cellz = info[0].boxL[2] / temp3;
567	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
568	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
569	>	n_per_extra = (int) ceil(temp1);
570	>
571	>	if (n_per_extra > 4){
572	>	sprintf(painCave.errMsg,
573	>	"SimSetup error. There has been an error in constructing"
574	>	" the non-complete lattice.\n");
575		painCave.isFatal = 1;
576		simError();
577		}
578		}
579		else{
580	<	n_cells = (int)temp3;
581	<	cellx = info->boxLx / temp3;
582	<	celly = info->boxLy / temp3;
583	<	cellz = info->boxLz / temp3;
580	>	n_cells = (int) temp3;
581	>	cellx = info[0].boxL[0] / temp3;
582	>	celly = info[0].boxL[1] / temp3;
583	>	cellz = info[0].boxL[2] / temp3;
584		}
585
586		current_mol = 0;
#	Line 645 | Line 588 | void SimSetup::initFromBass( void ){
588		current_comp = 0;
589		current_atom_ndx = 0;
590
591	<	for( i=0; i < n_cells ; i++ ){
592	<	for( j=0; j < n_cells; j++ ){
593	<	for( k=0; k < n_cells; k++ ){
591	>	for (i = 0; i < n_cells ; i++){
592	>	for (j = 0; j < n_cells; j++){
593	>	for (k = 0; k < n_cells; k++){
594	>	makeElement(i * cellx, j * celly, k * cellz);
595
596	<	makeElement( i * cellx,
653	<	j * celly,
654	<	k * cellz );
596	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
597
598	<	makeElement( i * cellx + 0.5 * cellx,
657	<	j * celly + 0.5 * celly,
658	<	k * cellz );
598	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
599
600	<	makeElement( i * cellx,
661	<	j * celly + 0.5 * celly,
662	<	k * cellz + 0.5 * cellz );
663	<
664	<	makeElement( i * cellx + 0.5 * cellx,
665	<	j * celly,
666	<	k * cellz + 0.5 * cellz );
600	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
601		}
602		}
603		}
604
605	<	if( have_extra ){
605	>	if (have_extra){
606		done = 0;
607
608		int start_ndx;
609	<	for( i=0; i < (n_cells+1) && !done; i++ ){
610	<	for( j=0; j < (n_cells+1) && !done; j++ ){
609	>	for (i = 0; i < (n_cells + 1) && !done; i++){
610	>	for (j = 0; j < (n_cells + 1) && !done; j++){
611	>	if (i < n_cells){
612	>	if (j < n_cells){
613	>	start_ndx = n_cells;
614	>	}
615	>	else
616	>	start_ndx = 0;
617	>	}
618	>	else
619	>	start_ndx = 0;
620
621	<	if( i < n_cells ){
621	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
622	>	makeElement(i * cellx, j * celly, k * cellz);
623	>	done = (current_mol >= tot_nmol);
624
625	<	if( j < n_cells ){
626	<	start_ndx = n_cells;
627	<	}
628	<	else start_ndx = 0;
629	<	}
685	<	else start_ndx = 0;
625	>	if (!done && n_per_extra > 1){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
627	>	k * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630
631	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
631	>	if (!done && n_per_extra > 2){
632	>	makeElement(i * cellx, j * celly + 0.5 * celly,
633	>	k * cellz + 0.5 * cellz);
634	>	done = (current_mol >= tot_nmol);
635	>	}
636
637	<	makeElement( i * cellx,
638	<	j * celly,
639	<	k * cellz );
640	<	done = ( current_mol >= tot_nmol );
641	<
642	<	if( !done && n_per_extra > 1 ){
695	<	makeElement( i * cellx + 0.5 * cellx,
696	<	j * celly + 0.5 * celly,
697	<	k * cellz );
698	<	done = ( current_mol >= tot_nmol );
699	<	}
700	<
701	<	if( !done && n_per_extra > 2){
702	<	makeElement( i * cellx,
703	<	j * celly + 0.5 * celly,
704	<	k * cellz + 0.5 * cellz );
705	<	done = ( current_mol >= tot_nmol );
706	<	}
707	<
708	<	if( !done && n_per_extra > 3){
709	<	makeElement( i * cellx + 0.5 * cellx,
710	<	j * celly,
711	<	k * cellz + 0.5 * cellz );
712	<	done = ( current_mol >= tot_nmol );
713	<	}
714	<	}
637	>	if (!done && n_per_extra > 3){
638	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642	>	}
643		}
644		}
645		}
646
647	<
648	<	for( i=0; i<info->n_atoms; i++ ){
721	<	info->atoms[i]->set_vx( 0.0 );
722	<	info->atoms[i]->set_vy( 0.0 );
723	<	info->atoms[i]->set_vz( 0.0 );
647	>	for (i = 0; i < info[0].n_atoms; i++){
648	>	info[0].atoms[i]->setVel(vel);
649		}
650		}
651
652	<	void SimSetup::makeElement( double x, double y, double z ){
728	<
652	>	void SimSetup::makeElement(double x, double y, double z){
653		int k;
654		AtomStamp* current_atom;
655		DirectionalAtom* dAtom;
656		double rotMat[3][3];
657	+	double pos[3];
658
659	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
659	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
660	>	current_atom = comp_stamps[current_comp]->getAtom(k);
661	>	if (!current_atom->havePosition()){
662	>	sprintf(painCave.errMsg,
663	>	"SimSetup:initFromBass error.\n"
664	>	"\tComponent %s, atom %s does not have a position specified.\n"
665	>	"\tThe initialization routine is unable to give a start"
666	>	" position.\n",
667	>	comp_stamps[current_comp]->getID(), current_atom->getType());
668	>	painCave.isFatal = 1;
669	>	simError();
670	>	}
671
672	<	current_atom = comp_stamps[current_comp]->getAtom( k );
673	<	if( !current_atom->havePosition() ){
674	<	sprintf( painCave.errMsg,
739	<	"SimSetup:initFromBass error.\n"
740	<	"\tComponent %s, atom %s does not have a position specified.\n"
741	<	"\tThe initialization routine is unable to give a start"
742	<	" position.\n",
743	<	comp_stamps[current_comp]->getID(),
744	<	current_atom->getType() );
745	<	painCave.isFatal = 1;
746	<	simError();
747	<	}
672	>	pos[0] = x + current_atom->getPosX();
673	>	pos[1] = y + current_atom->getPosY();
674	>	pos[2] = z + current_atom->getPosZ();
675
676	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
750	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
751	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
676	>	info[0].atoms[current_atom_ndx]->setPos(pos);
677
678	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
678	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
679	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
680
755	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
756	–
681		rotMat[0][0] = 1.0;
682		rotMat[0][1] = 0.0;
683		rotMat[0][2] = 0.0;
#	Line 766 | Line 690 | void SimSetup::makeElement( double x, double y, double
690		rotMat[2][1] = 0.0;
691		rotMat[2][2] = 1.0;
692
693	<	dAtom->setA( rotMat );
693	>	dAtom->setA(rotMat);
694		}
695
696		current_atom_ndx++;
#	Line 775 | Line 699 | void SimSetup::makeElement( double x, double y, double
699		current_mol++;
700		current_comp_mol++;
701
702	<	if( current_comp_mol >= components_nmol[current_comp] ){
779	<
702	>	if (current_comp_mol >= components_nmol[current_comp]){
703		current_comp_mol = 0;
704		current_comp++;
705		}
706		}
707
708
709	<	void SimSetup::gatherInfo( void ){
709	>	void SimSetup::gatherInfo(void){
710	>	int i;
711
712		ensembleCase = -1;
713		ffCase = -1;
714
791	–	// get the stamps and globals;
792	–	the_stamps = stamps;
793	–	the_globals = globals;
794	–
715		// set the easy ones first
796	–	info->target_temp = the_globals->getTargetTemp();
797	–	info->dt = the_globals->getDt();
798	–	info->run_time = the_globals->getRunTime();
799	–	n_components = the_globals->getNComponents();
716
717	+	for (i = 0; i < nInfo; i++){
718	+	info[i].target_temp = globals->getTargetTemp();
719	+	info[i].dt = globals->getDt();
720	+	info[i].run_time = globals->getRunTime();
721	+	}
722	+	n_components = globals->getNComponents();
723
724	+
725		// get the forceField
726
727	<	strcpy( force_field, the_globals->getForceField() );
727	>	strcpy(force_field, globals->getForceField());
728
729	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
730	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
729	>	if (!strcasecmp(force_field, "DUFF")){
730	>	ffCase = FF_DUFF;
731	>	}
732	>	else if (!strcasecmp(force_field, "LJ")){
733	>	ffCase = FF_LJ;
734	>	}
735	>	else if (!strcasecmp(force_field, "EAM")){
736	>	ffCase = FF_EAM;
737	>	}
738	>	else if (!strcasecmp(force_field, "WATER")){
739	>	ffCase = FF_H2O;
740	>	}
741		else{
742	<	sprintf( painCave.errMsg,
743	<	"SimSetup Error. Unrecognized force field -> %s\n",
744	<	force_field );
745	<	painCave.isFatal = 1;
813	<	simError();
742	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
743	>	force_field);
744	>	painCave.isFatal = 1;
745	>	simError();
746		}
747
748	<	// get the ensemble
748	>	// get the ensemble
749
750	<	strcpy( ensemble, the_globals->getEnsemble() );
750	>	strcpy(ensemble, globals->getEnsemble());
751
752	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
753	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
754	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
752	>	if (!strcasecmp(ensemble, "NVE")){
753	>	ensembleCase = NVE_ENS;
754	>	}
755	>	else if (!strcasecmp(ensemble, "NVT")){
756	>	ensembleCase = NVT_ENS;
757	>	}
758	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
759		ensembleCase = NPTi_ENS;
760	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
761	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
762	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
760	>	}
761	>	else if (!strcasecmp(ensemble, "NPTf")){
762	>	ensembleCase = NPTf_ENS;
763	>	}
764	>	else if (!strcasecmp(ensemble, "NPTxyz")){
765	>	ensembleCase = NPTxyz_ENS;
766	>	}
767		else{
768	<	sprintf( painCave.errMsg,
769	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
770	<	"reverting to NVE for this simulation.\n",
771	<	ensemble );
772	<	painCave.isFatal = 0;
773	<	simError();
774	<	strcpy( ensemble, "NVE" );
775	<	ensembleCase = NVE_ENS;
768	>	sprintf(painCave.errMsg,
769	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
770	>	"\treverting to NVE for this simulation.\n",
771	>	ensemble);
772	>	painCave.isFatal = 0;
773	>	simError();
774	>	strcpy(ensemble, "NVE");
775	>	ensembleCase = NVE_ENS;
776		}
837	–	strcpy( info->ensemble, ensemble );
777
778	<	// get the mixing rule
778	>	for (i = 0; i < nInfo; i++){
779	>	strcpy(info[i].ensemble, ensemble);
780
781	<	strcpy( info->mixingRule, the_globals->getMixingRule() );
782	<	info->usePBC = the_globals->getPBC();
783	<
784	<
781	>	// get the mixing rule
782	>
783	>	strcpy(info[i].mixingRule, globals->getMixingRule());
784	>	info[i].usePBC = globals->getPBC();
785	>	}
786	>
787		// get the components and calculate the tot_nMol and indvidual n_mol
788	<
789	<	the_components = the_globals->getComponents();
788	>
789	>	the_components = globals->getComponents();
790		components_nmol = new int[n_components];
791
792
793	<	if( !the_globals->haveNMol() ){
793	>	if (!globals->haveNMol()){
794		// we don't have the total number of molecules, so we assume it is
795		// given in each component
796
797		tot_nmol = 0;
798	<	for( i=0; i<n_components; i++ ){
799	<
800	<	if( !the_components[i]->haveNMol() ){
801	<	// we have a problem
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Error. No global NMol or component NMol"
804	<	" given. Cannot calculate the number of atoms.\n" );
805	<	painCave.isFatal = 1;
864	<	simError();
798	>	for (i = 0; i < n_components; i++){
799	>	if (!the_components[i]->haveNMol()){
800	>	// we have a problem
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup Error. No global NMol or component NMol given.\n"
803	>	"\tCannot calculate the number of atoms.\n");
804	>	painCave.isFatal = 1;
805	>	simError();
806		}
807
808		tot_nmol += the_components[i]->getNMol();
#	Line 869 | Line 810 | void SimSetup::gatherInfo( void ){
810		}
811		}
812		else{
813	<	sprintf( painCave.errMsg,
814	<	"SimSetup error.\n"
815	<	"\tSorry, the ability to specify total"
816	<	" nMols and then give molfractions in the components\n"
817	<	"\tis not currently supported."
818	<	" Please give nMol in the components.\n" );
813	>	sprintf(painCave.errMsg,
814	>	"SimSetup error.\n"
815	>	"\tSorry, the ability to specify total"
816	>	" nMols and then give molfractions in the components\n"
817	>	"\tis not currently supported."
818	>	" Please give nMol in the components.\n");
819		painCave.isFatal = 1;
820		simError();
821		}
822
823	<	// set the status, sample, and thermal kick times
824	<
825	<	if( the_globals->haveSampleTime() ){
826	<	info->sampleTime = the_globals->getSampleTime();
827	<	info->statusTime = info->sampleTime;
828	<	info->thermalTime = info->sampleTime;
823	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
824	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
825	>	sprintf(painCave.errMsg,
826	>	"Sample time is not divisible by dt.\n"
827	>	"\tThis will result in samples that are not uniformly\n"
828	>	"\tdistributed in time.  If this is a problem, change\n"
829	>	"\tyour sampleTime variable.\n");
830	>	painCave.isFatal = 0;
831	>	simError();
832		}
889	–	else{
890	–	info->sampleTime = the_globals->getRunTime();
891	–	info->statusTime = info->sampleTime;
892	–	info->thermalTime = info->sampleTime;
893	–	}
833
834	<	if( the_globals->haveStatusTime() ){
835	<	info->statusTime = the_globals->getStatusTime();
834	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
835	>	sprintf(painCave.errMsg,
836	>	"Status time is not divisible by dt.\n"
837	>	"\tThis will result in status reports that are not uniformly\n"
838	>	"\tdistributed in time.  If this is a problem, change \n"
839	>	"\tyour statusTime variable.\n");
840	>	painCave.isFatal = 0;
841	>	simError();
842		}
843
844	<	if( the_globals->haveThermalTime() ){
845	<	info->thermalTime = the_globals->getThermalTime();
846	<	}
844	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
845	>	sprintf(painCave.errMsg,
846	>	"Thermal time is not divisible by dt.\n"
847	>	"\tThis will result in thermalizations that are not uniformly\n"
848	>	"\tdistributed in time.  If this is a problem, change \n"
849	>	"\tyour thermalTime variable.\n");
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	}
853
854	<	// check for the temperature set flag
855	<
856	<	if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();
857	<
858	<	// get some of the tricky things that may still be in the globals
854	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
855	>	sprintf(painCave.errMsg,
856	>	"Reset time is not divisible by dt.\n"
857	>	"\tThis will result in integrator resets that are not uniformly\n"
858	>	"\tdistributed in time.  If this is a problem, change\n"
859	>	"\tyour resetTime variable.\n");
860	>	painCave.isFatal = 0;
861	>	simError();
862	>	}
863
864	<	double boxVector[3];
910	<	if( the_globals->haveBox() ){
911	<	boxVector[0] = the_globals->getBox();
912	<	boxVector[1] = the_globals->getBox();
913	<	boxVector[2] = the_globals->getBox();
914	<
915	<	info->setBox( boxVector );
916	<	}
917	<	else if( the_globals->haveDensity() ){
864	>	// set the status, sample, and thermal kick times
865
866	<	double vol;
867	<	vol = (double)tot_nmol / the_globals->getDensity();
868	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
869	<	boxVector[1] = boxVector[0];
870	<	boxVector[2] = boxVector[0];
866	>	for (i = 0; i < nInfo; i++){
867	>	if (globals->haveSampleTime()){
868	>	info[i].sampleTime = globals->getSampleTime();
869	>	info[i].statusTime = info[i].sampleTime;
870	>	info[i].thermalTime = info[i].sampleTime;
871	>	}
872	>	else{
873	>	info[i].sampleTime = globals->getRunTime();
874	>	info[i].statusTime = info[i].sampleTime;
875	>	info[i].thermalTime = info[i].sampleTime;
876	>	}
877
878	<	info->setBox( boxVector );
879	<	}
927	<	else{
928	<	if( !the_globals->haveBoxX() ){
929	<	sprintf( painCave.errMsg,
930	<	"SimSetup error, no periodic BoxX size given.\n" );
931	<	painCave.isFatal = 1;
932	<	simError();
878	>	if (globals->haveStatusTime()){
879	>	info[i].statusTime = globals->getStatusTime();
880		}
934	–	boxVector[0] = the_globals->getBoxX();
881
882	<	if( !the_globals->haveBoxY() ){
883	<	sprintf( painCave.errMsg,
938	<	"SimSetup error, no periodic BoxY size given.\n" );
939	<	painCave.isFatal = 1;
940	<	simError();
882	>	if (globals->haveThermalTime()){
883	>	info[i].thermalTime = globals->getThermalTime();
884		}
942	–	boxVector[1] = the_globals->getBoxY();
885
886	<	if( !the_globals->haveBoxZ() ){
887	<	sprintf( painCave.errMsg,
888	<	"SimSetup error, no periodic BoxZ size given.\n" );
889	<	painCave.isFatal = 1;
948	<	simError();
886	>	info[i].resetIntegrator = 0;
887	>	if( globals->haveResetTime() ){
888	>	info[i].resetTime = globals->getResetTime();
889	>	info[i].resetIntegrator = 1;
890		}
950	–	boxVector[2] = the_globals->getBoxZ();
891
892	<	info->setBox( boxVector );
892	>	// check for the temperature set flag
893	>
894	>	if (globals->haveTempSet())
895	>	info[i].setTemp = globals->getTempSet();
896	>
897	>	// check for the extended State init
898	>
899	>	info[i].useInitXSstate = globals->getUseInitXSstate();
900	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
901	>
902		}
903	+
904	+	//setup seed for random number generator
905	+	int seedValue;
906
907	+	if (globals->haveSeed()){
908	+	seedValue = globals->getSeed();
909
910	+	if(seedValue / 1E9 == 0){
911	+	sprintf(painCave.errMsg,
912	+	"Seed for sprng library should contain at least 9 digits\n"
913	+	"OOPSE will generate a seed for user\n");
914	+	painCave.isFatal = 0;
915	+	simError();
916	+
917	+	//using seed generated by system instead of invalid seed set by user
918	+	#ifndef IS_MPI
919	+	seedValue = make_sprng_seed();
920	+	#else
921	+	if (worldRank == 0){
922	+	seedValue = make_sprng_seed();
923	+	}
924	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	+	#endif
926	+	}
927	+	}//end of if branch of globals->haveSeed()
928	+	else{
929
930	+	#ifndef IS_MPI
931	+	seedValue = make_sprng_seed();
932	+	#else
933	+	if (worldRank == 0){
934	+	seedValue = make_sprng_seed();
935	+	}
936	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
937	+	#endif
938	+	}//end of globals->haveSeed()
939	+
940	+	for (int i = 0; i < nInfo; i++){
941	+	info[i].setSeed(seedValue);
942	+	}
943	+
944		#ifdef IS_MPI
945	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
945	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
946		MPIcheckPoint();
947		#endif // is_mpi
961	–
948		}
949
950
951	<	void SimSetup::finalInfoCheck( void ){
951	>	void SimSetup::finalInfoCheck(void){
952		int index;
953		int usesDipoles;
954	<
954	>	int i;
955
956	<	// check electrostatic parameters
957	<
958	<	index = 0;
959	<	usesDipoles = 0;
960	<	while( (index < info->n_atoms) && !usesDipoles ){
961	<	usesDipoles = ((info->atoms)[index])->hasDipole();
962	<	index++;
963	<	}
964	<
956	>	for (i = 0; i < nInfo; i++){
957	>	// check electrostatic parameters
958	>
959	>	index = 0;
960	>	usesDipoles = 0;
961	>	while ((index < info[i].n_atoms) && !usesDipoles){
962	>	usesDipoles = (info[i].atoms[index])->hasDipole();
963	>	index++;
964	>	}
965	>
966		#ifdef IS_MPI
967	<	int myUse = usesDipoles
968	<	MPI_Allreduce( &myUse, &UsesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
967	>	int myUse = usesDipoles;
968	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
969		#endif //is_mpi
970
971	+	double theEcr, theEst;
972
973	<	if (the_globals->getUseRF() ) {
974	<	info->useReactionField = 1;
987	<
988	<	if( !the_globals->haveECR() ){
989	<	sprintf( painCave.errMsg,
990	<	"SimSetup Warning: using default value of 1/2 the smallest "
991	<	"box length for the electrostaticCutoffRadius.\n"
992	<	"I hope you have a very fast processor!\n");
993	<	painCave.isFatal = 0;
994	<	simError();
995	<	double smallest;
996	<	smallest = info->boxLx;
997	<	if (info->boxLy <= smallest) smallest = info->boxLy;
998	<	if (info->boxLz <= smallest) smallest = info->boxLz;
999	<	info->ecr = 0.5 * smallest;
1000	<	} else {
1001	<	info->ecr        = the_globals->getECR();
1002	<	}
973	>	if (globals->getUseRF()){
974	>	info[i].useReactionField = 1;
975
976	<	if( !the_globals->haveEST() ){
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Warning: using default value of 0.05 * the "
979	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
980	<	);
1009	<	painCave.isFatal = 0;
1010	<	simError();
1011	<	info->est = 0.05 * info->ecr;
1012	<	} else {
1013	<	info->est        = the_globals->getEST();
1014	<	}
1015	<
1016	<	if(!the_globals->haveDielectric() ){
1017	<	sprintf( painCave.errMsg,
1018	<	"SimSetup Error: You are trying to use Reaction Field without"
1019	<	"setting a dielectric constant!\n"
1020	<	);
1021	<	painCave.isFatal = 1;
1022	<	simError();
1023	<	}
1024	<	info->dielectric = the_globals->getDielectric();
1025	<	}
1026	<	else {
1027	<	if (usesDipoles) {
1028	<
1029	<	if( !the_globals->haveECR() ){
1030	<	sprintf( painCave.errMsg,
1031	<	"SimSetup Warning: using default value of 1/2 the smallest "
1032	<	"box length for the electrostaticCutoffRadius.\n"
1033	<	"I hope you have a very fast processor!\n");
976	>	if (!globals->haveECR()){
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
979	>	"\tOOPSE will use a default value of 15.0 angstroms"
980	>	"\tfor the electrostaticCutoffRadius.\n");
981		painCave.isFatal = 0;
982		simError();
983	<	double smallest;
1037	<	smallest = info->boxLx;
1038	<	if (info->boxLy <= smallest) smallest = info->boxLy;
1039	<	if (info->boxLz <= smallest) smallest = info->boxLz;
1040	<	info->ecr = 0.5 * smallest;
1041	<	} else {
1042	<	info->ecr        = the_globals->getECR();
983	>	theEcr = 15.0;
984		}
985	<
986	<	if( !the_globals->haveEST() ){
987	<	sprintf( painCave.errMsg,
988	<	"SimSetup Warning: using default value of 5%% of the "
989	<	"electrostaticCutoffRadius for the "
990	<	"electrostaticSkinThickness\n"
991	<	);
985	>	else{
986	>	theEcr = globals->getECR();
987	>	}
988	>
989	>	if (!globals->haveEST()){
990	>	sprintf(painCave.errMsg,
991	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
992	>	"\tOOPSE will use a default value of\n"
993	>	"\t0.05 * electrostaticCutoffRadius\n"
994	>	"\tfor the electrostaticSkinThickness\n");
995		painCave.isFatal = 0;
996		simError();
997	<	info->est = 0.05 * info->ecr;
1054	<	} else {
1055	<	info->est        = the_globals->getEST();
997	>	theEst = 0.05 * theEcr;
998		}
999	<	}
1000	<	}
999	>	else{
1000	>	theEst = globals->getEST();
1001	>	}
1002
1003	+	info[i].setDefaultEcr(theEcr, theEst);
1004	+
1005	+	if (!globals->haveDielectric()){
1006	+	sprintf(painCave.errMsg,
1007	+	"SimSetup Error: No Dielectric constant was set.\n"
1008	+	"\tYou are trying to use Reaction Field without"
1009	+	"\tsetting a dielectric constant!\n");
1010	+	painCave.isFatal = 1;
1011	+	simError();
1012	+	}
1013	+	info[i].dielectric = globals->getDielectric();
1014	+	}
1015	+	else{
1016	+	if (usesDipoles){
1017	+	if (!globals->haveECR()){
1018	+	sprintf(painCave.errMsg,
1019	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1020	+	"\tOOPSE will use a default value of 15.0 angstroms"
1021	+	"\tfor the electrostaticCutoffRadius.\n");
1022	+	painCave.isFatal = 0;
1023	+	simError();
1024	+	theEcr = 15.0;
1025	+	}
1026	+	else{
1027	+	theEcr = globals->getECR();
1028	+	}
1029	+
1030	+	if (!globals->haveEST()){
1031	+	sprintf(painCave.errMsg,
1032	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1033	+	"\tOOPSE will use a default value of\n"
1034	+	"\t0.05 * electrostaticCutoffRadius\n"
1035	+	"\tfor the electrostaticSkinThickness\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	theEst = 0.05 * theEcr;
1039	+	}
1040	+	else{
1041	+	theEst = globals->getEST();
1042	+	}
1043	+
1044	+	info[i].setDefaultEcr(theEcr, theEst);
1045	+	}
1046	+	}
1047	+	}
1048		#ifdef IS_MPI
1049	<	strcpy( checkPointMsg, "post processing checks out" );
1049	>	strcpy(checkPointMsg, "post processing checks out");
1050		MPIcheckPoint();
1051		#endif // is_mpi
1064	–
1052		}
1053	+
1054	+	void SimSetup::initSystemCoords(void){
1055	+	int i;
1056
1057	<	void SimSetup::initSystemCoords( void ){
1057	>	char* inName;
1058
1059	<	if( the_globals->haveInitialConfig() ){
1060	<
1061	<	InitializeFromFile* fileInit;
1059	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1060	>
1061	>	for (i = 0; i < info[0].n_atoms; i++)
1062	>	info[0].atoms[i]->setCoords();
1063	>
1064	>	if (globals->haveInitialConfig()){
1065	>	InitializeFromFile* fileInit;
1066		#ifdef IS_MPI // is_mpi
1067	<	if( worldRank == 0 ){
1067	>	if (worldRank == 0){
1068		#endif //is_mpi
1069	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
1069	>	inName = globals->getInitialConfig();
1070	>	fileInit = new InitializeFromFile(inName);
1071		#ifdef IS_MPI
1072	<	}else fileInit = new InitializeFromFile( NULL );
1072	>	}
1073	>	else
1074	>	fileInit = new InitializeFromFile(NULL);
1075		#endif
1076	<	fileInit->read_xyz( info ); // default velocities on
1076	>	fileInit->readInit(info); // default velocities on
1077
1078	<	delete fileInit;
1079	<	}
1080	<	else{
1078	>	delete fileInit;
1079	>	}
1080	>	else{
1081	>
1082	>	// no init from bass
1083	>
1084	>	sprintf(painCave.errMsg,
1085	>	"Cannot intialize a simulation without an initial configuration file.\n");
1086	>	painCave.isFatal = 1;;
1087	>	simError();
1088	>
1089	>	}
1090
1085	–	#ifdef IS_MPI
1086	–
1087	–	// no init from bass
1088	–
1089	–	sprintf( painCave.errMsg,
1090	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
1091	–	painCave.isFatal;
1092	–	simError();
1093	–
1094	–	#else
1095	–
1096	–	initFromBass();
1097	–
1098	–
1099	–	#endif
1100	–	}
1101	–
1091		#ifdef IS_MPI
1092	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1092	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1093		MPIcheckPoint();
1094		#endif // is_mpi
1106	–
1095		}
1096
1097
1098	<	void SimSetup::makeOutNames( void ){
1098	>	void SimSetup::makeOutNames(void){
1099	>	int k;
1100
1101	+
1102	+	for (k = 0; k < nInfo; k++){
1103		#ifdef IS_MPI
1104	<	if( worldRank == 0 ){
1104	>	if (worldRank == 0){
1105		#endif // is_mpi
1106	<
1107	<	if( the_globals->haveFinalConfig() ){
1108	<	strcpy( info->finalName, the_globals->getFinalConfig() );
1118	<	}
1119	<	else{
1120	<	strcpy( info->finalName, inFileName );
1121	<	char* endTest;
1122	<	int nameLength = strlen( info->finalName );
1123	<	endTest = &(info->finalName[nameLength - 5]);
1124	<	if( !strcmp( endTest, ".bass" ) ){
1125	<	strcpy( endTest, ".eor" );
1106	>
1107	>	if (globals->haveFinalConfig()){
1108	>	strcpy(info[k].finalName, globals->getFinalConfig());
1109		}
1127	–	else if( !strcmp( endTest, ".BASS" ) ){
1128	–	strcpy( endTest, ".eor" );
1129	–	}
1110		else{
1111	<	endTest = &(info->finalName[nameLength - 4]);
1112	<	if( !strcmp( endTest, ".bss" ) ){
1113	<	strcpy( endTest, ".eor" );
1114	<	}
1115	<	else if( !strcmp( endTest, ".mdl" ) ){
1116	<	strcpy( endTest, ".eor" );
1117	<	}
1118	<	else{
1119	<	strcat( info->finalName, ".eor" );
1120	<	}
1111	>	strcpy(info[k].finalName, inFileName);
1112	>	char* endTest;
1113	>	int nameLength = strlen(info[k].finalName);
1114	>	endTest = &(info[k].finalName[nameLength - 5]);
1115	>	if (!strcmp(endTest, ".bass")){
1116	>	strcpy(endTest, ".eor");
1117	>	}
1118	>	else if (!strcmp(endTest, ".BASS")){
1119	>	strcpy(endTest, ".eor");
1120	>	}
1121	>	else{
1122	>	endTest = &(info[k].finalName[nameLength - 4]);
1123	>	if (!strcmp(endTest, ".bss")){
1124	>	strcpy(endTest, ".eor");
1125	>	}
1126	>	else if (!strcmp(endTest, ".mdl")){
1127	>	strcpy(endTest, ".eor");
1128	>	}
1129	>	else{
1130	>	strcat(info[k].finalName, ".eor");
1131	>	}
1132	>	}
1133		}
1134	<	}
1135	<
1136	<	// make the sample and status out names
1137	<
1138	<	strcpy( info->sampleName, inFileName );
1139	<	char* endTest;
1140	<	int nameLength = strlen( info->sampleName );
1141	<	endTest = &(info->sampleName[nameLength - 5]);
1142	<	if( !strcmp( endTest, ".bass" ) ){
1151	<	strcpy( endTest, ".dump" );
1152	<	}
1153	<	else if( !strcmp( endTest, ".BASS" ) ){
1154	<	strcpy( endTest, ".dump" );
1155	<	}
1156	<	else{
1157	<	endTest = &(info->sampleName[nameLength - 4]);
1158	<	if( !strcmp( endTest, ".bss" ) ){
1159	<	strcpy( endTest, ".dump" );
1134	>
1135	>	// make the sample and status out names
1136	>
1137	>	strcpy(info[k].sampleName, inFileName);
1138	>	char* endTest;
1139	>	int nameLength = strlen(info[k].sampleName);
1140	>	endTest = &(info[k].sampleName[nameLength - 5]);
1141	>	if (!strcmp(endTest, ".bass")){
1142	>	strcpy(endTest, ".dump");
1143		}
1144	<	else if( !strcmp( endTest, ".mdl" ) ){
1145	<	strcpy( endTest, ".dump" );
1144	>	else if (!strcmp(endTest, ".BASS")){
1145	>	strcpy(endTest, ".dump");
1146		}
1147		else{
1148	<	strcat( info->sampleName, ".dump" );
1148	>	endTest = &(info[k].sampleName[nameLength - 4]);
1149	>	if (!strcmp(endTest, ".bss")){
1150	>	strcpy(endTest, ".dump");
1151	>	}
1152	>	else if (!strcmp(endTest, ".mdl")){
1153	>	strcpy(endTest, ".dump");
1154	>	}
1155	>	else{
1156	>	strcat(info[k].sampleName, ".dump");
1157	>	}
1158		}
1159	<	}
1160	<
1161	<	strcpy( info->statusName, inFileName );
1162	<	nameLength = strlen( info->statusName );
1163	<	endTest = &(info->statusName[nameLength - 5]);
1164	<	if( !strcmp( endTest, ".bass" ) ){
1173	<	strcpy( endTest, ".stat" );
1174	<	}
1175	<	else if( !strcmp( endTest, ".BASS" ) ){
1176	<	strcpy( endTest, ".stat" );
1177	<	}
1178	<	else{
1179	<	endTest = &(info->statusName[nameLength - 4]);
1180	<	if( !strcmp( endTest, ".bss" ) ){
1181	<	strcpy( endTest, ".stat" );
1159	>
1160	>	strcpy(info[k].statusName, inFileName);
1161	>	nameLength = strlen(info[k].statusName);
1162	>	endTest = &(info[k].statusName[nameLength - 5]);
1163	>	if (!strcmp(endTest, ".bass")){
1164	>	strcpy(endTest, ".stat");
1165		}
1166	<	else if( !strcmp( endTest, ".mdl" ) ){
1167	<	strcpy( endTest, ".stat" );
1166	>	else if (!strcmp(endTest, ".BASS")){
1167	>	strcpy(endTest, ".stat");
1168		}
1169		else{
1170	<	strcat( info->statusName, ".stat" );
1170	>	endTest = &(info[k].statusName[nameLength - 4]);
1171	>	if (!strcmp(endTest, ".bss")){
1172	>	strcpy(endTest, ".stat");
1173	>	}
1174	>	else if (!strcmp(endTest, ".mdl")){
1175	>	strcpy(endTest, ".stat");
1176	>	}
1177	>	else{
1178	>	strcat(info[k].statusName, ".stat");
1179	>	}
1180		}
1181	<	}
1190	<
1181	>
1182		#ifdef IS_MPI
1192	–	}
1193	–	#endif // is_mpi
1183
1184	+	}
1185	+	#endif // is_mpi
1186	+	}
1187		}
1188
1189
1190	<	void SimSetup::sysObjectsCreation( void ){
1190	>	void SimSetup::sysObjectsCreation(void){
1191	>	int i, k;
1192
1193		// create the forceField
1194
#	Line 1211 | Line 1204 | void SimSetup::sysObjectsCreation( void ){
1204
1205		#ifdef IS_MPI
1206		// divide the molecules among the processors
1207	<
1207	>
1208		mpiMolDivide();
1209		#endif //is_mpi
1210	<
1210	>
1211		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1212	<
1212	>
1213		makeSysArrays();
1214
1215	<
1215	>	// make and initialize the molecules (all but atomic coordinates)
1216
1217	+	makeMolecules();
1218
1219	+	for (k = 0; k < nInfo; k++){
1220	+	info[k].identArray = new int[info[k].n_atoms];
1221	+	for (i = 0; i < info[k].n_atoms; i++){
1222	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1223	+	}
1224	+	}
1225		}
1226
1227
1228	<	void SimSetup::createFF( void ){
1228	>	void SimSetup::createFF(void){
1229	>	switch (ffCase){
1230	>	case FF_DUFF:
1231	>	the_ff = new DUFF();
1232	>	break;
1233
1234	<	switch( ffCase ){
1234	>	case FF_LJ:
1235	>	the_ff = new LJFF();
1236	>	break;
1237
1238	<	case FF_DUFF:
1239	<	the_ff = new DUFF();
1240	<	break;
1238	>	case FF_EAM:
1239	>	the_ff = new EAM_FF();
1240	>	break;
1241
1242	<	case FF_LJ:
1243	<	the_ff = new LJFF();
1244	<	break;
1242	>	case FF_H2O:
1243	>	the_ff = new WATER();
1244	>	break;
1245
1246	<	default:
1247	<	sprintf( painCave.errMsg,
1248	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1249	<	painCave.isFatal = 1;
1250	<	simError();
1246	>	default:
1247	>	sprintf(painCave.errMsg,
1248	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1249	>	painCave.isFatal = 1;
1250	>	simError();
1251		}
1252
1253		#ifdef IS_MPI
1254	<	strcpy( checkPointMsg, "ForceField creation successful" );
1254	>	strcpy(checkPointMsg, "ForceField creation successful");
1255		MPIcheckPoint();
1256		#endif // is_mpi
1251	–
1257		}
1258
1259
1260	<	void SimSetup::compList( void ){
1260	>	void SimSetup::compList(void){
1261	>	int i;
1262	>	char* id;
1263	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1264	>	LinkedMolStamp* currentStamp = NULL;
1265	>	comp_stamps = new MoleculeStamp * [n_components];
1266
1257	–	comp_stamps = new MoleculeStamp*[n_components];
1258	–
1267		// make an array of molecule stamps that match the components used.
1268		// also extract the used stamps out into a separate linked list
1269
1270	<	info->nComponents = n_components;
1271	<	info->componentsNmol = components_nmol;
1272	<	info->compStamps = comp_stamps;
1273	<	info->headStamp = new LinkedMolStamp();
1274	<
1275	<	char* id;
1268	<	LinkedMolStamp* headStamp = info->headStamp;
1269	<	LinkedMolStamp* currentStamp = NULL;
1270	<	for( i=0; i<n_components; i++ ){
1270	>	for (i = 0; i < nInfo; i++){
1271	>	info[i].nComponents = n_components;
1272	>	info[i].componentsNmol = components_nmol;
1273	>	info[i].compStamps = comp_stamps;
1274	>	info[i].headStamp = headStamp;
1275	>	}
1276
1277	+
1278	+	for (i = 0; i < n_components; i++){
1279		id = the_components[i]->getType();
1280		comp_stamps[i] = NULL;
1281	<
1281	>
1282		// check to make sure the component isn't already in the list
1283
1284	<	comp_stamps[i] = headStamp->match( id );
1285	<	if( comp_stamps[i] == NULL ){
1279	<
1284	>	comp_stamps[i] = headStamp->match(id);
1285	>	if (comp_stamps[i] == NULL){
1286		// extract the component from the list;
1287	<
1288	<	currentStamp = the_stamps->extractMolStamp( id );
1289	<	if( currentStamp == NULL ){
1290	<	sprintf( painCave.errMsg,
1291	<	"SimSetup error: Component \"%s\" was not found in the "
1292	<	"list of declared molecules\n",
1293	<	id );
1294	<	painCave.isFatal = 1;
1295	<	simError();
1287	>
1288	>	currentStamp = stamps->extractMolStamp(id);
1289	>	if (currentStamp == NULL){
1290	>	sprintf(painCave.errMsg,
1291	>	"SimSetup error: Component \"%s\" was not found in the "
1292	>	"list of declared molecules\n",
1293	>	id);
1294	>	painCave.isFatal = 1;
1295	>	simError();
1296		}
1297	<
1298	<	headStamp->add( currentStamp );
1299	<	comp_stamps[i] = headStamp->match( id );
1297	>
1298	>	headStamp->add(currentStamp);
1299	>	comp_stamps[i] = headStamp->match(id);
1300		}
1301		}
1302
1303		#ifdef IS_MPI
1304	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1304	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1305		MPIcheckPoint();
1306		#endif // is_mpi
1301	–
1302	–
1307		}
1308
1309	<	void SimSetup::calcSysValues( void ){
1309	>	void SimSetup::calcSysValues(void){
1310	>	int i;
1311
1312	+	int* molMembershipArray;
1313	+
1314		tot_atoms = 0;
1315		tot_bonds = 0;
1316		tot_bends = 0;
1317		tot_torsions = 0;
1318	<	for( i=0; i<n_components; i++ ){
1319	<
1320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1318	>	tot_rigid = 0;
1319	>	for (i = 0; i < n_components; i++){
1320	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1321	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1322	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1323		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1324	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1325		}
1326	<
1326	>
1327		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1328	+	molMembershipArray = new int[tot_atoms];
1329
1330	<	info->n_atoms = tot_atoms;
1331	<	info->n_bonds = tot_bonds;
1332	<	info->n_bends = tot_bends;
1333	<	info->n_torsions = tot_torsions;
1334	<	info->n_SRI = tot_SRI;
1335	<	info->n_mol = tot_nmol;
1336	<
1337	<	info->molMembershipArray = new int[tot_atoms];
1330	>	for (i = 0; i < nInfo; i++){
1331	>	info[i].n_atoms = tot_atoms;
1332	>	info[i].n_bonds = tot_bonds;
1333	>	info[i].n_bends = tot_bends;
1334	>	info[i].n_torsions = tot_torsions;
1335	>	info[i].n_SRI = tot_SRI;
1336	>	info[i].n_mol = tot_nmol;
1337	>
1338	>	info[i].molMembershipArray = molMembershipArray;
1339	>	}
1340		}
1341
1331	–
1342		#ifdef IS_MPI
1343
1344	<	void SimSetup::mpiMolDivide( void ){
1345	<
1344	>	void SimSetup::mpiMolDivide(void){
1345	>	int i, j, k;
1346		int localMol, allMol;
1347		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1348	+	int local_rigid;
1349
1350	<	mpiSim = new mpiSimulation( info );
1351	<
1350	>	mpiSim = new mpiSimulation(info);
1351	>
1352		globalIndex = mpiSim->divideLabor();
1353
1354		// set up the local variables
1355	<
1355	>
1356		mol2proc = mpiSim->getMolToProcMap();
1357		molCompType = mpiSim->getMolComponentType();
1358	<
1358	>
1359		allMol = 0;
1360		localMol = 0;
1361		local_atoms = 0;
1362		local_bonds = 0;
1363		local_bends = 0;
1364		local_torsions = 0;
1365	+	local_rigid = 0;
1366		globalAtomIndex = 0;
1367
1368	<
1369	<	for( i=0; i<n_components; i++ ){
1370	<
1371	<	for( j=0; j<components_nmol[i]; j++ ){
1372	<
1373	<	if( mol2proc[allMol] == worldRank ){
1374	<
1375	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1376	<	local_bonds +=    comp_stamps[i]->getNBonds();
1365	<	local_bends +=    comp_stamps[i]->getNBends();
1366	<	local_torsions += comp_stamps[i]->getNTorsions();
1367	<	localMol++;
1368	>	for (i = 0; i < n_components; i++){
1369	>	for (j = 0; j < components_nmol[i]; j++){
1370	>	if (mol2proc[allMol] == worldRank){
1371	>	local_atoms += comp_stamps[i]->getNAtoms();
1372	>	local_bonds += comp_stamps[i]->getNBonds();
1373	>	local_bends += comp_stamps[i]->getNBends();
1374	>	local_torsions += comp_stamps[i]->getNTorsions();
1375	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1376	>	localMol++;
1377		}
1378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1379	<	info->molMembershipArray[globalAtomIndex] = allMol;
1378	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1379	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1380		globalAtomIndex++;
1381		}
1382
1383	<	allMol++;
1383	>	allMol++;
1384		}
1385		}
1386		local_SRI = local_bonds + local_bends + local_torsions;
1387	+
1388	+	info[0].n_atoms = mpiSim->getMyNlocal();
1389
1390	<	info->n_atoms = mpiSim->getMyNlocal();
1391	<
1392	<	if( local_atoms != info->n_atoms ){
1393	<	sprintf( painCave.errMsg,
1394	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1395	<	" localAtom (%d) are not equal.\n",
1385	<	info->n_atoms,
1386	<	local_atoms );
1390	>
1391	>	if (local_atoms != info[0].n_atoms){
1392	>	sprintf(painCave.errMsg,
1393	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1394	>	"\tlocalAtom (%d) are not equal.\n",
1395	>	info[0].n_atoms, local_atoms);
1396		painCave.isFatal = 1;
1397		simError();
1398		}
1399
1400	<	info->n_bonds = local_bonds;
1401	<	info->n_bends = local_bends;
1402	<	info->n_torsions = local_torsions;
1403	<	info->n_SRI = local_SRI;
1404	<	info->n_mol = localMol;
1400	>	info[0].n_bonds = local_bonds;
1401	>	info[0].n_bends = local_bends;
1402	>	info[0].n_torsions = local_torsions;
1403	>	info[0].n_SRI = local_SRI;
1404	>	info[0].n_mol = localMol;
1405
1406	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1406	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1407		MPIcheckPoint();
1408		}
1409	<
1409	>
1410		#endif // is_mpi
1411
1412
1413	<	void SimSetup::makeSysArrays( void ){
1414	<
1415	<	// create the atom and short range interaction arrays
1413	>	void SimSetup::makeSysArrays(void){
1414	>
1415	>	#ifndef IS_MPI
1416	>	int k, j;
1417	>	#endif // is_mpi
1418	>	int i, l;
1419
1420	<	Atom::createArrays(info->n_atoms);
1421	<	the_atoms = new Atom*[info->n_atoms];
1410	<	the_molecules = new Molecule[info->n_mol];
1411	<	int molIndex;
1420	>	Atom** the_atoms;
1421	>	Molecule* the_molecules;
1422
1423	<	// initialize the molecule's stampID's
1423	>	for (l = 0; l < nInfo; l++){
1424	>	// create the atom and short range interaction arrays
1425
1426	+	the_atoms = new Atom * [info[l].n_atoms];
1427	+	the_molecules = new Molecule[info[l].n_mol];
1428	+	int molIndex;
1429	+
1430	+	// initialize the molecule's stampID's
1431	+
1432		#ifdef IS_MPI
1416	–
1433
1434	<	molIndex = 0;
1435	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1436	<
1437	<	if(mol2proc[i] == worldRank ){
1438	<	the_molecules[molIndex].setStampID( molCompType[i] );
1439	<	the_molecules[molIndex].setMyIndex( molIndex );
1440	<	the_molecules[molIndex].setGlobalIndex( i );
1441	<	molIndex++;
1434	>
1435	>	molIndex = 0;
1436	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1437	>	if (mol2proc[i] == worldRank){
1438	>	the_molecules[molIndex].setStampID(molCompType[i]);
1439	>	the_molecules[molIndex].setMyIndex(molIndex);
1440	>	the_molecules[molIndex].setGlobalIndex(i);
1441	>	molIndex++;
1442	>	}
1443		}
1427	–	}
1444
1445		#else // is_mpi
1446	<
1447	<	molIndex = 0;
1448	<	globalAtomIndex = 0;
1449	<	for(i=0; i<n_components; i++){
1450	<	for(j=0; j<components_nmol[i]; j++ ){
1451	<	the_molecules[molIndex].setStampID( i );
1452	<	the_molecules[molIndex].setMyIndex( molIndex );
1453	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1454	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1455	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1456	<	globalAtomIndex++;
1446	>
1447	>	molIndex = 0;
1448	>	globalAtomIndex = 0;
1449	>	for (i = 0; i < n_components; i++){
1450	>	for (j = 0; j < components_nmol[i]; j++){
1451	>	the_molecules[molIndex].setStampID(i);
1452	>	the_molecules[molIndex].setMyIndex(molIndex);
1453	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1454	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1455	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1456	>	globalAtomIndex++;
1457	>	}
1458	>	molIndex++;
1459		}
1442	–	molIndex++;
1460		}
1461	<	}
1461	>
1462	>
1463	>	#endif // is_mpi
1464	>
1465	>	info[l].globalExcludes = new int;
1466	>	info[l].globalExcludes[0] = 0;
1467
1468	+	// set the arrays into the SimInfo object
1469
1470	+	info[l].atoms = the_atoms;
1471	+	info[l].molecules = the_molecules;
1472	+	info[l].nGlobalExcludes = 0;
1473	+
1474	+	the_ff->setSimInfo(info);
1475	+	}
1476	+	}
1477	+
1478	+	void SimSetup::makeIntegrator(void){
1479	+	int k;
1480	+
1481	+	NVE<RealIntegrator>* myNVE = NULL;
1482	+	NVT<RealIntegrator>* myNVT = NULL;
1483	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1484	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1485	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1486	+
1487	+	for (k = 0; k < nInfo; k++){
1488	+	switch (ensembleCase){
1489	+	case NVE_ENS:
1490	+	if (globals->haveZconstraints()){
1491	+	setupZConstraint(info[k]);
1492	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1493	+	}
1494	+	else{
1495	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1496	+	}
1497	+
1498	+	info->the_integrator = myNVE;
1499	+	break;
1500	+
1501	+	case NVT_ENS:
1502	+	if (globals->haveZconstraints()){
1503	+	setupZConstraint(info[k]);
1504	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1505	+	}
1506	+	else
1507	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1508	+
1509	+	myNVT->setTargetTemp(globals->getTargetTemp());
1510	+
1511	+	if (globals->haveTauThermostat())
1512	+	myNVT->setTauThermostat(globals->getTauThermostat());
1513	+	else{
1514	+	sprintf(painCave.errMsg,
1515	+	"SimSetup error: If you use the NVT\n"
1516	+	"\tensemble, you must set tauThermostat.\n");
1517	+	painCave.isFatal = 1;
1518	+	simError();
1519	+	}
1520	+
1521	+	info->the_integrator = myNVT;
1522	+	break;
1523	+
1524	+	case NPTi_ENS:
1525	+	if (globals->haveZconstraints()){
1526	+	setupZConstraint(info[k]);
1527	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1528	+	}
1529	+	else
1530	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1531	+
1532	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1533	+
1534	+	if (globals->haveTargetPressure())
1535	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1536	+	else{
1537	+	sprintf(painCave.errMsg,
1538	+	"SimSetup error: If you use a constant pressure\n"
1539	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+
1544	+	if (globals->haveTauThermostat())
1545	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1546	+	else{
1547	+	sprintf(painCave.errMsg,
1548	+	"SimSetup error: If you use an NPT\n"
1549	+	"\tensemble, you must set tauThermostat.\n");
1550	+	painCave.isFatal = 1;
1551	+	simError();
1552	+	}
1553	+
1554	+	if (globals->haveTauBarostat())
1555	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1556	+	else{
1557	+	sprintf(painCave.errMsg,
1558	+	"SimSetup error: If you use an NPT\n"
1559	+	"\tensemble, you must set tauBarostat.\n");
1560	+	painCave.isFatal = 1;
1561	+	simError();
1562	+	}
1563	+
1564	+	info->the_integrator = myNPTi;
1565	+	break;
1566	+
1567	+	case NPTf_ENS:
1568	+	if (globals->haveZconstraints()){
1569	+	setupZConstraint(info[k]);
1570	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1571	+	}
1572	+	else
1573	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1574	+
1575	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1576	+
1577	+	if (globals->haveTargetPressure())
1578	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1579	+	else{
1580	+	sprintf(painCave.errMsg,
1581	+	"SimSetup error: If you use a constant pressure\n"
1582	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1583	+	painCave.isFatal = 1;
1584	+	simError();
1585	+	}
1586	+
1587	+	if (globals->haveTauThermostat())
1588	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1589	+
1590	+	else{
1591	+	sprintf(painCave.errMsg,
1592	+	"SimSetup error: If you use an NPT\n"
1593	+	"\tensemble, you must set tauThermostat.\n");
1594	+	painCave.isFatal = 1;
1595	+	simError();
1596	+	}
1597	+
1598	+	if (globals->haveTauBarostat())
1599	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1600	+
1601	+	else{
1602	+	sprintf(painCave.errMsg,
1603	+	"SimSetup error: If you use an NPT\n"
1604	+	"\tensemble, you must set tauBarostat.\n");
1605	+	painCave.isFatal = 1;
1606	+	simError();
1607	+	}
1608	+
1609	+	info->the_integrator = myNPTf;
1610	+	break;
1611	+
1612	+	case NPTxyz_ENS:
1613	+	if (globals->haveZconstraints()){
1614	+	setupZConstraint(info[k]);
1615	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1616	+	}
1617	+	else
1618	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1619	+
1620	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1621	+
1622	+	if (globals->haveTargetPressure())
1623	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1624	+	else{
1625	+	sprintf(painCave.errMsg,
1626	+	"SimSetup error: If you use a constant pressure\n"
1627	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1628	+	painCave.isFatal = 1;
1629	+	simError();
1630	+	}
1631	+
1632	+	if (globals->haveTauThermostat())
1633	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1634	+	else{
1635	+	sprintf(painCave.errMsg,
1636	+	"SimSetup error: If you use an NPT\n"
1637	+	"\tensemble, you must set tauThermostat.\n");
1638	+	painCave.isFatal = 1;
1639	+	simError();
1640	+	}
1641	+
1642	+	if (globals->haveTauBarostat())
1643	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1644	+	else{
1645	+	sprintf(painCave.errMsg,
1646	+	"SimSetup error: If you use an NPT\n"
1647	+	"\tensemble, you must set tauBarostat.\n");
1648	+	painCave.isFatal = 1;
1649	+	simError();
1650	+	}
1651	+
1652	+	info->the_integrator = myNPTxyz;
1653	+	break;
1654	+
1655	+	default:
1656	+	sprintf(painCave.errMsg,
1657	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1658	+	painCave.isFatal = 1;
1659	+	simError();
1660	+	}
1661	+	}
1662	+	}
1663	+
1664	+	void SimSetup::initFortran(void){
1665	+	info[0].refreshSim();
1666	+
1667	+	if (!strcmp(info[0].mixingRule, "standard")){
1668	+	the_ff->initForceField(LB_MIXING_RULE);
1669	+	}
1670	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1671	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1672	+	}
1673	+	else{
1674	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1675	+	info[0].mixingRule);
1676	+	painCave.isFatal = 1;
1677	+	simError();
1678	+	}
1679	+
1680	+
1681	+	#ifdef IS_MPI
1682	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1683	+	MPIcheckPoint();
1684		#endif // is_mpi
1685	+	}
1686
1687	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1688	+	int nZConstraints;
1689	+	ZconStamp** zconStamp;
1690
1691	<	if( info->n_SRI ){
1692	<
1693	<	Exclude::createArray(info->n_SRI);
1694	<	the_excludes = new Exclude*[info->n_SRI];
1695	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1696	<	info->globalExcludes = new int;
1456	<	info->n_exclude = info->n_SRI;
1691	>	if (globals->haveZconstraintTime()){
1692	>	//add sample time of z-constraint  into SimInfo's property list
1693	>	DoubleData* zconsTimeProp = new DoubleData();
1694	>	zconsTimeProp->setID(ZCONSTIME_ID);
1695	>	zconsTimeProp->setData(globals->getZconsTime());
1696	>	theInfo.addProperty(zconsTimeProp);
1697		}
1698		else{
1699	<
1700	<	Exclude::createArray( 1 );
1701	<	the_excludes = new Exclude*;
1702	<	the_excludes[0] = new Exclude(0);
1703	<	the_excludes[0]->setPair( 0,0 );
1464	<	info->globalExcludes = new int;
1465	<	info->globalExcludes[0] = 0;
1466	<	info->n_exclude = 0;
1699	>	sprintf(painCave.errMsg,
1700	>	"ZConstraint error: If you use a ZConstraint,\n"
1701	>	"\tyou must set zconsTime.\n");
1702	>	painCave.isFatal = 1;
1703	>	simError();
1704		}
1705
1706	<	// set the arrays into the SimInfo object
1706	>	//push zconsTol into siminfo, if user does not specify
1707	>	//value for zconsTol, a default value will be used
1708	>	DoubleData* zconsTol = new DoubleData();
1709	>	zconsTol->setID(ZCONSTOL_ID);
1710	>	if (globals->haveZconsTol()){
1711	>	zconsTol->setData(globals->getZconsTol());
1712	>	}
1713	>	else{
1714	>	double defaultZConsTol = 0.01;
1715	>	sprintf(painCave.errMsg,
1716	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1717	>	"\tOOPSE will use a default value of %f.\n"
1718	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1719	>	defaultZConsTol);
1720	>	painCave.isFatal = 0;
1721	>	simError();
1722
1723	<	info->atoms = the_atoms;
1724	<	info->molecules = the_molecules;
1725	<	info->nGlobalExcludes = 0;
1474	<	info->excludes = the_excludes;
1723	>	zconsTol->setData(defaultZConsTol);
1724	>	}
1725	>	theInfo.addProperty(zconsTol);
1726
1727	<	the_ff->setSimInfo( info );
1727	>	//set Force Subtraction Policy
1728	>	StringData* zconsForcePolicy = new StringData();
1729	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1730
1731	+	if (globals->haveZconsForcePolicy()){
1732	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1733	+	}
1734	+	else{
1735	+	sprintf(painCave.errMsg,
1736	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1737	+	"\tOOPSE will use PolicyByMass.\n"
1738	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1739	+	painCave.isFatal = 0;
1740	+	simError();
1741	+	zconsForcePolicy->setData("BYMASS");
1742	+	}
1743	+
1744	+	theInfo.addProperty(zconsForcePolicy);
1745	+
1746	+	//set zcons gap
1747	+	DoubleData* zconsGap = new DoubleData();
1748	+	zconsGap->setID(ZCONSGAP_ID);
1749	+
1750	+	if (globals->haveZConsGap()){
1751	+	zconsGap->setData(globals->getZconsGap());
1752	+	theInfo.addProperty(zconsGap);
1753	+	}
1754	+
1755	+	//set zcons fixtime
1756	+	DoubleData* zconsFixtime = new DoubleData();
1757	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1758	+
1759	+	if (globals->haveZConsFixTime()){
1760	+	zconsFixtime->setData(globals->getZconsFixtime());
1761	+	theInfo.addProperty(zconsFixtime);
1762	+	}
1763	+
1764	+	//set zconsUsingSMD
1765	+	IntData* zconsUsingSMD = new IntData();
1766	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1767	+
1768	+	if (globals->haveZConsUsingSMD()){
1769	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1770	+	theInfo.addProperty(zconsUsingSMD);
1771	+	}
1772	+
1773	+	//Determine the name of ouput file and add it into SimInfo's property list
1774	+	//Be careful, do not use inFileName, since it is a pointer which
1775	+	//point to a string at master node, and slave nodes do not contain that string
1776	+
1777	+	string zconsOutput(theInfo.finalName);
1778	+
1779	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1780	+
1781	+	StringData* zconsFilename = new StringData();
1782	+	zconsFilename->setID(ZCONSFILENAME_ID);
1783	+	zconsFilename->setData(zconsOutput);
1784	+
1785	+	theInfo.addProperty(zconsFilename);
1786	+
1787	+	//setup index, pos and other parameters of z-constraint molecules
1788	+	nZConstraints = globals->getNzConstraints();
1789	+	theInfo.nZconstraints = nZConstraints;
1790	+
1791	+	zconStamp = globals->getZconStamp();
1792	+	ZConsParaItem tempParaItem;
1793	+
1794	+	ZConsParaData* zconsParaData = new ZConsParaData();
1795	+	zconsParaData->setID(ZCONSPARADATA_ID);
1796	+
1797	+	for (int i = 0; i < nZConstraints; i++){
1798	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1799	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1800	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1801	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1802	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1803	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1804	+	zconsParaData->addItem(tempParaItem);
1805	+	}
1806	+
1807	+	//check the uniqueness of index
1808	+	if(!zconsParaData->isIndexUnique()){
1809	+	sprintf(painCave.errMsg,
1810	+	"ZConstraint Error: molIndex is not unique!\n");
1811	+	painCave.isFatal = 1;
1812	+	simError();
1813	+	}
1814	+
1815	+	//sort the parameters by index of molecules
1816	+	zconsParaData->sortByIndex();
1817	+
1818	+	//push data into siminfo, therefore, we can retrieve later
1819	+	theInfo.addProperty(zconsParaData);
1820		}
1821	+
1822	+	void SimSetup::makeMinimizer(){
1823	+
1824	+	OOPSEMinimizer* myOOPSEMinimizer;
1825	+	MinimizerParameterSet* param;
1826	+	char minimizerName[100];
1827	+
1828	+	for (int i = 0; i < nInfo; i++){
1829	+
1830	+	//prepare parameter set for minimizer
1831	+	param = new MinimizerParameterSet();
1832	+	param->setDefaultParameter();
1833	+
1834	+	if (globals->haveMinimizer()){
1835	+	param->setFTol(globals->getMinFTol());
1836	+	}
1837	+
1838	+	if (globals->haveMinGTol()){
1839	+	param->setGTol(globals->getMinGTol());
1840	+	}
1841	+
1842	+	if (globals->haveMinMaxIter()){
1843	+	param->setMaxIteration(globals->getMinMaxIter());
1844	+	}
1845	+
1846	+	if (globals->haveMinWriteFrq()){
1847	+	param->setMaxIteration(globals->getMinMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinWriteFrq()){
1851	+	param->setWriteFrq(globals->getMinWriteFrq());
1852	+	}
1853	+
1854	+	if (globals->haveMinStepSize()){
1855	+	param->setStepSize(globals->getMinStepSize());
1856	+	}
1857	+
1858	+	if (globals->haveMinLSMaxIter()){
1859	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1860	+	}
1861	+
1862	+	if (globals->haveMinLSTol()){
1863	+	param->setLineSearchTol(globals->getMinLSTol());
1864	+	}
1865	+
1866	+	strcpy(minimizerName, globals->getMinimizer());
1867	+
1868	+	if (!strcasecmp(minimizerName, "CG")){
1869	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870	+	}
1871	+	else if (!strcasecmp(minimizerName, "SD")){
1872	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1873	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1874	+	}
1875	+	else{
1876	+	sprintf(painCave.errMsg,
1877	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1878	+	painCave.isFatal = 0;
1879	+	simError();
1880	+
1881	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1882	+	}
1883	+	info[i].the_integrator = myOOPSEMinimizer;
1884	+
1885	+	//store the minimizer into simInfo
1886	+	info[i].the_minimizer = myOOPSEMinimizer;
1887	+	info[i].has_minimizer = true;
1888	+	}
1889	+
1890	+	}

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