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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 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"
18		#include "mpiSimulation.hpp"
19		#endif
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 NPTxyz_ENS     4
28	+
29	+
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 27 | 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();
59	<	mpiEventLoop();
60	<
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
126	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
132	>	sysObjectsCreation();
133
134	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
134	>	// check on the post processing info
135
136	+	finalInfoCheck();
137
138	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
138	>	// initialize the system coordinates
139
140	<	#ifdef IS_MPI
141	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
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();
150
151	+	#ifdef IS_MPI
152	+	mpiSim->mpiRefresh();
153	+	#endif
154
155	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
155	>	// initialize the Fortran
156
157	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
157	>	initFortran();
158
159	<	tot_nmol = 0;
160	<	for( i=0; i<n_components; i++ ){
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
166	>	}
167
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
168
169	<	#ifdef IS_MPI
170	<	strcpy( checkPointMsg, "Have the number of components" );
171	<	MPIcheckPoint();
172	<	#endif // is_mpi
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	// make an array of molecule stamps that match the components used.
192	<	// also extract the used stamps out into a separate linked list
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194
195	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
195	>	set<int> skipList;
196
197	<	id = the_components[i]->getType();
198	<	comp_stamps[i] = NULL;
199	<
181	<	// check to make sure the component isn't already in the list
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200
201	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
201	>	//init the forceField paramters
202
203	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
203	>	the_ff->readParams();
204
205	+	// init the atoms
206
207	+	int nMembers, nNew, rb1, rb2;
208
209	<	// caclulate the number of atoms, bonds, bends and torsions
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211
212	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
212	>	atomOffset = 0;
213
214	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	simnfo->n_atoms = tot_atoms;
219	<	simnfo->n_bonds = tot_bonds;
220	<	simnfo->n_bends = tot_bends;
221	<	simnfo->n_torsions = tot_torsions;
222	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	<
225	<	#ifdef IS_MPI
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	>
226	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
227
228	<	// divide the molecules among processors here.
229	<
230	<	mpiSim = new mpiSimulation( simnfo );
231	<
241	<
228	>	if (molInfo.nBonds > 0)
229	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	>	else
231	>	molInfo.myBonds = NULL;
232
233	<	globalIndex = mpiSim->divideLabor();
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new Bend*[molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237
238	+	if (molInfo.nTorsions > 0)
239	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	+	else
241	+	molInfo.myTorsions = NULL;
242
243	<
244	<	// set up the local variables
245	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
247	>	// make the Atoms
248
249	<	simnfo->n_atoms = mpiSim->getMyNlocal();
250	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	<	simnfo->n_bonds = local_bonds;
253	<	simnfo->n_bends = local_bends;
254	<	simnfo->n_torsions = local_torsions;
255	<	simnfo->n_SRI = local_SRI;
256	<	simnfo->n_mol = localMol;
252	>	if (currentAtom->haveOrientation()){
253	>	dAtom = new DirectionalAtom((j + atomOffset),
254	>	info[k].getConfiguration());
255	>	info[k].n_oriented++;
256	>	molInfo.myAtoms[j] = dAtom;
257
258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
259	<	MPIcheckPoint();
260	<
298	<
299	<	#endif // is_mpi
300	<
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261
262	<	// create the atom and short range interaction arrays
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	Atom::createArrays(simnfo->n_atoms);
267	<	the_atoms = new Atom*[simnfo->n_atoms];
268	<	the_molecules = new Molecule[simnfo->n_mol];
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	<	if( simnfo->n_SRI ){
310	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
273	>	}
274
275	<	simnfo->n_exclude = 1;
276	<	}
275	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
276	>	#ifdef IS_MPI
277
278	<	// set the arrays into the SimInfo object
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280	<	simnfo->atoms = the_atoms;
281	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
280	>	#endif // is_mpi
281	>	}
282
283	+	// make the bonds
284	+	for (j = 0; j < molInfo.nBonds; j++){
285	+	currentBond = comp_stamps[stampID]->getBond(j);
286	+	theBonds[j].a = currentBond->getA() + atomOffset;
287	+	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	// get some of the tricky things that may still be in the globals
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
336	–
337	–	if( the_globals->haveBox() ){
338	–	simnfo->box_x = the_globals->getBox();
339	–	simnfo->box_y = the_globals->getBox();
340	–	simnfo->box_z = the_globals->getBox();
341	–	}
342	–	else if( the_globals->haveDensity() ){
343	–
344	–	double vol;
345	–	vol = (double)tot_nmol / the_globals->getDensity();
346	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	–	simnfo->box_y = simnfo->box_x;
348	–	simnfo->box_z = simnfo->box_x;
349	–	}
350	–	else{
351	–	if( !the_globals->haveBoxX() ){
352	–	sprintf( painCave.errMsg,
353	–	"SimSetup error, no periodic BoxX size given.\n" );
354	–	painCave.isFatal = 1;
355	–	simError();
356	–	}
357	–	simnfo->box_x = the_globals->getBoxX();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
292		#ifdef IS_MPI
293	<	strcpy( checkPointMsg, "Box size set up" );
294	<	MPIcheckPoint();
295	<	#endif // is_mpi
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	+	info[k].excludes->addPair(exI, exJ);
301	+	}
302
303	<	// initialize the arrays
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<	the_ff->setSimInfo( simnfo );
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	makeAtoms();
315	<	simnfo->identArray = new int[simnfo->n_atoms];
316	<	for(i=0; i<simnfo->n_atoms; i++){
317	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
318	<	}
319	<
320	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	if( tot_bends ){
323	<	makeBends();
324	<	}
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	<	if( tot_torsions ){
329	<	makeTorsions();
330	<	}
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350
351	<	if (the_globals->getUseRF() ) {
352	<	simnfo->useReactionField = 1;
353	<
354	<	if( !the_globals->haveECR() ){
355	<	sprintf( painCave.errMsg,
356	<	"SimSetup Warning: using default value of 1/2 the smallest "
357	<	"box length for the electrostaticCutoffRadius.\n"
358	<	"I hope you have a very fast processor!\n");
359	<	painCave.isFatal = 0;
360	<	simError();
361	<	double smallest;
362	<	smallest = simnfo->box_x;
363	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
351	>	if (theBends[j].isGhost) {
352	>
353	>	tempI = theBends[j].a;
354	>	tempJ = theBends[j].b;
355	>
356	>	#ifdef IS_MPI
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
365	>	} else {
366
367	+	tempI = theBends[j].a;
368	+	tempJ = theBends[j].b;
369	+	tempK = theBends[j].c;
370	+
371		#ifdef IS_MPI
372	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
373	<	MPIcheckPoint();
374	<	#endif // is_mpi
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385	>	}
386
387	<	if( the_globals->haveInitialConfig() ){
388	<
389	<	InitializeFromFile* fileInit;
390	<	#ifdef IS_MPI // is_mpi
391	<	if( worldRank == 0 ){
392	<	#endif //is_mpi
393	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393	>
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398	>
399		#ifdef IS_MPI
400	<	}else fileInit = new InitializeFromFile( NULL );
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
410
411	<	delete fileInit;
412	<	}
413	<	else{
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	<	#ifdef IS_MPI
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	<	// no init from bass
425	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426
427	<	initFromBass();
427	>	// Create the Rigid Body:
428
429	+	myRB = new RigidBody();
430
431	<	#endif
432	<	}
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438
439	+	// tempI is atom numbering on local processor
440	+	tempI = molI + atomOffset;
441
442	<
443	<
444	<
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445
446	<
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452		#ifdef IS_MPI
453	<	if( worldRank == 0 ){
454	<	#endif // is_mpi
455	<
456	<	if( the_globals->haveFinalConfig() ){
457	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
458	<	}
459	<	else{
460	<	strcpy( simnfo->finalName, inFileName );
461	<	char* endTest;
462	<	int nameLength = strlen( simnfo->finalName );
463	<	endTest = &(simnfo->finalName[nameLength - 5]);
464	<	if( !strcmp( endTest, ".bass" ) ){
465	<	strcpy( endTest, ".eor" );
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487		}
488	<	else if( !strcmp( endTest, ".BASS" ) ){
489	<	strcpy( endTest, ".eor" );
490	<	}
491	<	else{
492	<	endTest = &(simnfo->finalName[nameLength - 4]);
493	<	if( !strcmp( endTest, ".bss" ) ){
494	<	strcpy( endTest, ".eor" );
495	<	}
496	<	else if( !strcmp( endTest, ".mdl" ) ){
497	<	strcpy( endTest, ".eor" );
498	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
608	<	}
609	<	#endif // is_mpi
610	<
611	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
617	<	}
618	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
488	>
489	>
490	>	//create cutoff group for molecule
491	>
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499
500	<	if( the_globals->haveStatusTime() ){
501	<	simnfo->statusTime = the_globals->getStatusTime();
502	<	}
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503
504	<	if( the_globals->haveThermalTime() ){
505	<	simnfo->thermalTime = the_globals->getThermalTime();
630	<	}
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506
507	<	// check for the temperature set flag
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511
512	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514
515	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517
518	<	//   // make the longe range forces and the integrator
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519
520	<	//   new AllLong( simnfo );
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521
522	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
523	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
524	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
525	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528	>	}
529
530	+
531
532
533	<	// initialize the Fortran
534	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
654	<	}
655	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	<	}
658	<	else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
662	<	painCave.isFatal = 1;
663	<	simError();
664	<	}
533	>	// After this is all set up, scan through the atoms to
534	>	// see if they can be added to the integrableObjects:
535
536	+	molInfo.myIntegrableObjects.clear();
537	+
538
539	+	for (j = 0; j < molInfo.nAtoms; j++){
540	+
541		#ifdef IS_MPI
542	<	strcpy( checkPointMsg,
543	<	"Successfully intialized the mixingRule for Fortran." );
544	<	MPIcheckPoint();
545	<	#endif // is_mpi
672	<	}
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545	>	#endif
546
547	+	// if they aren't on the skip list, then they can be integrated
548
549	<	void SimSetup::makeMolecules( void ){
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
684	<
685	<	//init the forceField paramters
556	>	// all rigid bodies are integrated:
557
558	<	the_ff->readParams();
559	<
560	<
561	<	// init the molecules
691	<
692	<	atomOffset = 0;
693	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
696	<
697	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	<	info.nBends    = comp_stamps[stampID]->getNBends();
700	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	<
702	<	info.myAtoms = &the_atoms[atomOffset];
703	<	info.myBonds = new Bond*[info.nBonds];
704	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
706	<
707	<	theBonds = new bond_pair[info.nBonds];
708	<	theBends = new bend_set[info.nBends];
709	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
714	<
715	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562		}
737	–	else{
738	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	–	}
740	–	info.myAtoms[j]->setType( currentAtom->getType() );
563
742	–	#ifdef IS_MPI
564
565	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
565	>	// send the arrays off to the forceField for init.
566
567	<	#endif // is_mpi
568	<	}
569	<
570	<	// make the bonds
571	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	<	exI = theBonds[i].a;
757	<	exJ = theBonds[i].b;
573	>	info[k].molecules[i].initialize(molInfo);
574
759	–	// exclude_I must always be the smaller of the pair
760	–	if( exI > exJ ){
761	–	tempEx = exI;
762	–	exI = exJ;
763	–	exJ = tempEx;
764	–	}
765	–	#ifdef IS_MPI
766	–
767	–	the_excludes[index*2] =
768	–	the_atoms[exI]->getGlobalIndex() + 1;
769	–	the_excludes[index*2 + 1] =
770	–	the_atoms[exJ]->getGlobalIndex() + 1;
771	–
772	–	#else  // isn't MPI
773	–
774	–	the_excludes[index*2] =     exI + 1;
775	–	the_excludes[index*2 + 1] = exJ + 1;
776	–	// fortran index from 1 (hence the +1 in the indexing)
575
576	<	#endif  //is_mpi
577	<
578	<	}
579	<
580	<
783	<
784	<
785	<
786	<
787	<
788	<
789	<
790	<
791	<
792	<
793	<
794	<
795	<
796	<	void SimSetup::makeAtoms( void ){
797	<
798	<	int i, j, k, index;
799	<	double ux, uy, uz, uSqr, u;
800	<	AtomStamp* current_atom;
801	<
802	<	DirectionalAtom* dAtom;
803	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
804	<
805	<	lMolIndex = 0;
806	<	molIndex = 0;
807	<	index = 0;
808	<	for( i=0; i<n_components; i++ ){
809	<
810	<	for( j=0; j<components_nmol[i]; j++ ){
811	<
812	<	#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
816	<
817	<	molStart = index;
818	<	nMemb = comp_stamps[i]->getNAtoms();
819	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
820	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
859	<
860	<	#ifdef IS_MPI
861	<	}
862	<	#endif //is_mpi
863	<
864	<	molIndex++;
865	<	}
866	<	}
867	<
868	<	#ifdef IS_MPI
869	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
870	<
871	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
877	<	}
878	<
879	<	void SimSetup::makeBonds( void ){
880	<
881	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882	<	bond_pair* the_bonds;
883	<	BondStamp* current_bond;
884	<
885	<	the_bonds = new bond_pair[tot_bonds];
886	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
889	<
890	<	for( i=0; i<n_components; i++ ){
891	<
892	<	for( j=0; j<components_nmol[i]; j++ ){
893	<
894	<	#ifdef IS_MPI
895	<	if( mpiSim->getMyMolStart() <= molIndex &&
896	<	molIndex <= mpiSim->getMyMolEnd() ){
897	<	#endif // is_mpi
898	<
899	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
904	<
905	<	exI = the_bonds[index].a;
906	<	exJ = the_bonds[index].b;
907	<
908	<	// exclude_I must always be the smaller of the pair
909	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
914	<
915	<
916	<	#ifdef IS_MPI
917	<
918	<	the_excludes[index*2] =
919	<	the_atoms[exI]->getGlobalIndex() + 1;
920	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
922	<
923	<	#else  // isn't MPI
924	<
925	<	the_excludes[index*2] =     exI + 1;
926	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
936	<	}
937	<	#endif //is_mpi
938	<
939	<	molIndex++;
940	<	}
941	<	}
942	<
943	<	the_ff->initializeBonds( the_bonds );
944	<	}
945	<
946	<	void SimSetup::makeBends( void ){
947	<
948	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
954	<
955	<	the_bends = new bend_set[tot_bends];
956	<	index = 0;
957	<	offset = 0;
958	<	molIndex = 0;
959	<	for( i=0; i<n_components; i++ ){
960	<
961	<	for( j=0; j<components_nmol[i]; j++ ){
962	<
963	<	#ifdef IS_MPI
964	<	if( mpiSim->getMyMolStart() <= molIndex &&
965	<	molIndex <= mpiSim->getMyMolEnd() ){
966	<	#endif // is_mpi
967	<
968	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
969	<
970	<	current_bend = comp_stamps[i]->getBend( k );
971	<	the_bends[index].a = current_bend->getA() + offset;
972	<	the_bends[index].b = current_bend->getB() + offset;
973	<	the_bends[index].c = current_bend->getC() + offset;
974	<
975	<	if( current_bend->haveExtras() ){
976	<
977	<	extras = current_bend->getExtras();
978	<	current_extra = extras;
979	<
980	<	while( current_extra != NULL ){
981	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	<
983	<	switch( current_extra->getType() ){
984	<
985	<	case 0:
986	<	the_bends[index].ghost =
987	<	current_extra->getInt() + offset;
988	<	the_bends[index].isGhost = 1;
989	<	break;
990	<
991	<	case 1:
992	<	the_bends[index].ghost =
993	<	(int)current_extra->getDouble() + offset;
994	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
1040	<
1041	<
1042	<	#ifdef IS_MPI
1043	<
1044	<	the_excludes[(index + tot_bonds)*2] =
1045	<	the_atoms[exI]->getGlobalIndex() + 1;
1046	<	the_excludes[(index + tot_bonds)*2 + 1] =
1047	<	the_atoms[exJ]->getGlobalIndex() + 1;
1048	<
1049	<	#else  // isn't MPI
1050	<
1051	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	<	// fortran index from 1 (hence the +1 in the indexing)
1054	<	#endif  //is_mpi
1055	<
1056	<
1057	<	// increment the index and repeat;
1058	<	index++;
1059	<	}
1060	<	offset += comp_stamps[i]->getNAtoms();
1061	<
1062	<	#ifdef IS_MPI
1063	<	}
1064	<	#endif //is_mpi
1065	<
1066	<	molIndex++;
1067	<	}
576	>	atomOffset += molInfo.nAtoms;
577	>	delete[] theBonds;
578	>	delete[] theBends;
579	>	delete[] theTorsions;
580	>	}
581		}
582
583		#ifdef IS_MPI
584	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
1075	–
587
1077	–	the_ff->initializeBends( the_bends );
588		}
589
590	<	void SimSetup::makeTorsions( void ){
1081	<
1082	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
1085	<
1086	<	the_torsions = new torsion_set[tot_torsions];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1091	<
1092	<	for( j=0; j<components_nmol[i]; j++ ){
1093	<
1094	<	#ifdef IS_MPI
1095	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1098	<
1099	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1100	<
1101	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1106	<
1107	<	exI = the_torsions[index].a;
1108	<	exJ = the_torsions[index].d;
1109	<
1110	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1117	<
1118	<
1119	<	#ifdef IS_MPI
1120	<
1121	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1122	<	the_atoms[exI]->getGlobalIndex() + 1;
1123	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124	<	the_atoms[exJ]->getGlobalIndex() + 1;
1125	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1133	<
1134	<	// increment the index and repeat;
1135	<	index++;
1136	<	}
1137	<	offset += comp_stamps[i]->getNAtoms();
1138	<
1139	<	#ifdef IS_MPI
1140	<	}
1141	<	#endif //is_mpi
1142	<
1143	<	molIndex++;
1144	<	}
1145	<	}
1146	<
1147	<	the_ff->initializeTorsions( the_torsions );
1148	<	}
1149	<
1150	<	void SimSetup::initFromBass( void ){
1151	<
590	>	void SimSetup::initFromBass(void){
591		int i, j, k;
592		int n_cells;
593		double cellx, celly, cellz;
#	Line 1157 | Line 596 | void SimSetup::initFromBass( void ){
596		int n_extra;
597		int have_extra, done;
598
599	<	temp1 = (double)tot_nmol / 4.0;
600	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
601	<	temp3 = ceil( temp2 );
599	>	double vel[3];
600	>	vel[0] = 0.0;
601	>	vel[1] = 0.0;
602	>	vel[2] = 0.0;
603
604	<	have_extra =0;
605	<	if( temp2 < temp3 ){ // we have a non-complete lattice
606	<	have_extra =1;
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607
608	<	n_cells = (int)temp3 - 1;
609	<	cellx = simnfo->box_x / temp3;
610	<	celly = simnfo->box_y / temp3;
611	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612
613	<	if( n_per_extra > 4){
614	<	sprintf( painCave.errMsg,
615	<	"SimSetup error. There has been an error in constructing"
616	<	" the non-complete lattice.\n" );
613	>	n_cells = (int) temp3 - 1;
614	>	cellx = info[0].boxL[0] / temp3;
615	>	celly = info[0].boxL[1] / temp3;
616	>	cellz = info[0].boxL[2] / temp3;
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620	>
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625		painCave.isFatal = 1;
626		simError();
627		}
628		}
629		else{
630	<	n_cells = (int)temp3;
631	<	cellx = simnfo->box_x / temp3;
632	<	celly = simnfo->box_y / temp3;
633	<	cellz = simnfo->box_z / temp3;
630	>	n_cells = (int) temp3;
631	>	cellx = info[0].boxL[0] / temp3;
632	>	celly = info[0].boxL[1] / temp3;
633	>	cellz = info[0].boxL[2] / temp3;
634		}
635
636		current_mol = 0;
#	Line 1193 | Line 638 | void SimSetup::initFromBass( void ){
638		current_comp = 0;
639		current_atom_ndx = 0;
640
641	<	for( i=0; i < n_cells ; i++ ){
642	<	for( j=0; j < n_cells; j++ ){
643	<	for( k=0; k < n_cells; k++ ){
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645
646	<	makeElement( i * cellx,
1201	<	j * celly,
1202	<	k * cellz );
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	makeElement( i * cellx + 0.5 * cellx,
1205	<	j * celly + 0.5 * celly,
1206	<	k * cellz );
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	<	makeElement( i * cellx,
1209	<	j * celly + 0.5 * celly,
1210	<	k * cellz + 0.5 * cellz );
1211	<
1212	<	makeElement( i * cellx + 0.5 * cellx,
1213	<	j * celly,
1214	<	k * cellz + 0.5 * cellz );
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651		}
652		}
653		}
654
655	<	if( have_extra ){
655	>	if (have_extra){
656		done = 0;
657
658		int start_ndx;
659	<	for( i=0; i < (n_cells+1) && !done; i++ ){
660	<	for( j=0; j < (n_cells+1) && !done; j++ ){
661	<
662	<	if( i < n_cells ){
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	if( j < n_cells ){
672	<	start_ndx = n_cells;
673	<	}
1231	<	else start_ndx = 0;
1232	<	}
1233	<	else start_ndx = 0;
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	makeElement( i * cellx,
682	<	j * celly,
683	<	k * cellz );
684	<	done = ( current_mol >= tot_nmol );
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	if( !done && n_per_extra > 1 ){
688	<	makeElement( i * cellx + 0.5 * cellx,
689	<	j * celly + 0.5 * celly,
690	<	k * cellz );
691	<	done = ( current_mol >= tot_nmol );
692	<	}
1248	<
1249	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1255	<
1256	<	if( !done && n_per_extra > 3){
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly,
1259	<	k * cellz + 0.5 * cellz );
1260	<	done = ( current_mol >= tot_nmol );
1261	<	}
1262	<	}
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693		}
694		}
695		}
696
697	<
698	<	for( i=0; i<simnfo->n_atoms; i++ ){
1269	<	simnfo->atoms[i]->set_vx( 0.0 );
1270	<	simnfo->atoms[i]->set_vy( 0.0 );
1271	<	simnfo->atoms[i]->set_vz( 0.0 );
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699		}
700		}
701
702	<	void SimSetup::makeElement( double x, double y, double z ){
1276	<
702	>	void SimSetup::makeElement(double x, double y, double z){
703		int k;
704		AtomStamp* current_atom;
705		DirectionalAtom* dAtom;
706		double rotMat[3][3];
707	+	double pos[3];
708
709	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
710	<
711	<	current_atom = comp_stamps[current_comp]->getAtom( k );
712	<	if( !current_atom->havePosition() ){
713	<	sprintf( painCave.errMsg,
714	<	"SimSetup:initFromBass error.\n"
715	<	"\tComponent %s, atom %s does not have a position specified.\n"
716	<	"\tThe initialization routine is unable to give a start"
717	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
721
722	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
723	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
724	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731		rotMat[0][0] = 1.0;
732		rotMat[0][1] = 0.0;
#	Line 1314 | Line 740 | void SimSetup::makeElement( double x, double y, double
740		rotMat[2][1] = 0.0;
741		rotMat[2][2] = 1.0;
742
743	<	dAtom->setA( rotMat );
743	>	dAtom->setA(rotMat);
744		}
745
746		current_atom_ndx++;
747	+	}
748	+
749	+	current_mol++;
750	+	current_comp_mol++;
751	+
752	+	if (current_comp_mol >= components_nmol[current_comp]){
753	+	current_comp_mol = 0;
754	+	current_comp++;
755	+	}
756	+	}
757	+
758	+
759	+	void SimSetup::gatherInfo(void){
760	+	int i;
761	+
762	+	ensembleCase = -1;
763	+	ffCase = -1;
764	+
765	+	// set the easy ones first
766	+
767	+	for (i = 0; i < nInfo; i++){
768	+	info[i].target_temp = globals->getTargetTemp();
769	+	info[i].dt = globals->getDt();
770	+	info[i].run_time = globals->getRunTime();
771	+	}
772	+	n_components = globals->getNComponents();
773	+
774	+
775	+	// get the forceField
776	+
777	+	strcpy(force_field, globals->getForceField());
778	+
779	+	if (!strcasecmp(force_field, "DUFF")){
780	+	ffCase = FF_DUFF;
781	+	}
782	+	else if (!strcasecmp(force_field, "LJ")){
783	+	ffCase = FF_LJ;
784	+	}
785	+	else if (!strcasecmp(force_field, "EAM")){
786	+	ffCase = FF_EAM;
787	+	}
788	+	else if (!strcasecmp(force_field, "WATER")){
789	+	ffCase = FF_H2O;
790	+	}
791	+	else{
792	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	+	force_field);
794	+	painCave.isFatal = 1;
795	+	simError();
796	+	}
797	+
798	+	// get the ensemble
799	+
800	+	strcpy(ensemble, globals->getEnsemble());
801	+
802	+	if (!strcasecmp(ensemble, "NVE")){
803	+	ensembleCase = NVE_ENS;
804	+	}
805	+	else if (!strcasecmp(ensemble, "NVT")){
806	+	ensembleCase = NVT_ENS;
807	+	}
808	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	+	ensembleCase = NPTi_ENS;
810	+	}
811	+	else if (!strcasecmp(ensemble, "NPTf")){
812	+	ensembleCase = NPTf_ENS;
813	+	}
814	+	else if (!strcasecmp(ensemble, "NPTxyz")){
815	+	ensembleCase = NPTxyz_ENS;
816	+	}
817	+	else{
818	+	sprintf(painCave.errMsg,
819	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	+	"\treverting to NVE for this simulation.\n",
821	+	ensemble);
822	+	painCave.isFatal = 0;
823	+	simError();
824	+	strcpy(ensemble, "NVE");
825	+	ensembleCase = NVE_ENS;
826	+	}
827	+
828	+	for (i = 0; i < nInfo; i++){
829	+	strcpy(info[i].ensemble, ensemble);
830	+
831	+	// get the mixing rule
832	+
833	+	strcpy(info[i].mixingRule, globals->getMixingRule());
834	+	info[i].usePBC = globals->getPBC();
835	+	}
836	+
837	+	// get the components and calculate the tot_nMol and indvidual n_mol
838	+
839	+	the_components = globals->getComponents();
840	+	components_nmol = new int[n_components];
841	+
842	+
843	+	if (!globals->haveNMol()){
844	+	// we don't have the total number of molecules, so we assume it is
845	+	// given in each component
846	+
847	+	tot_nmol = 0;
848	+	for (i = 0; i < n_components; i++){
849	+	if (!the_components[i]->haveNMol()){
850	+	// we have a problem
851	+	sprintf(painCave.errMsg,
852	+	"SimSetup Error. No global NMol or component NMol given.\n"
853	+	"\tCannot calculate the number of atoms.\n");
854	+	painCave.isFatal = 1;
855	+	simError();
856	+	}
857	+
858	+	tot_nmol += the_components[i]->getNMol();
859	+	components_nmol[i] = the_components[i]->getNMol();
860	+	}
861	+	}
862	+	else{
863	+	sprintf(painCave.errMsg,
864	+	"SimSetup error.\n"
865	+	"\tSorry, the ability to specify total"
866	+	" nMols and then give molfractions in the components\n"
867	+	"\tis not currently supported."
868	+	" Please give nMol in the components.\n");
869	+	painCave.isFatal = 1;
870	+	simError();
871	+	}
872	+
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903	+
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914	+	// set the status, sample, and thermal kick times
915	+
916	+	for (i = 0; i < nInfo; i++){
917	+	if (globals->haveSampleTime()){
918	+	info[i].sampleTime = globals->getSampleTime();
919	+	info[i].statusTime = info[i].sampleTime;
920	+	}
921	+	else{
922	+	info[i].sampleTime = globals->getRunTime();
923	+	info[i].statusTime = info[i].sampleTime;
924	+	}
925	+
926	+	if (globals->haveStatusTime()){
927	+	info[i].statusTime = globals->getStatusTime();
928	+	}
929	+
930	+	if (globals->haveThermalTime()){
931	+	info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934	+	}
935	+
936	+	info[i].resetIntegrator = 0;
937	+	if( globals->haveResetTime() ){
938	+	info[i].resetTime = globals->getResetTime();
939	+	info[i].resetIntegrator = 1;
940	+	}
941	+
942	+	// check for the temperature set flag
943	+
944	+	if (globals->haveTempSet())
945	+	info[i].setTemp = globals->getTempSet();
946	+
947	+	// check for the extended State init
948	+
949	+	info[i].useInitXSstate = globals->getUseInitXSstate();
950	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	+
952	+	// check for thermodynamic integration
953	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
954	+	info[i].thermIntLambda = globals->getThermIntLambda();
955	+	info[i].thermIntK = globals->getThermIntK();
956	+	info[i].useThermInt = 1;
957	+
958	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
959	+	info[i].restraint = myRestraint;
960	+	}
961	+	}
962	+
963	+	//setup seed for random number generator
964	+	int seedValue;
965	+
966	+	if (globals->haveSeed()){
967	+	seedValue = globals->getSeed();
968	+
969	+	if(seedValue / 1E9 == 0){
970	+	sprintf(painCave.errMsg,
971	+	"Seed for sprng library should contain at least 9 digits\n"
972	+	"OOPSE will generate a seed for user\n");
973	+	painCave.isFatal = 0;
974	+	simError();
975	+
976	+	//using seed generated by system instead of invalid seed set by user
977	+	#ifndef IS_MPI
978	+	seedValue = make_sprng_seed();
979	+	#else
980	+	if (worldRank == 0){
981	+	seedValue = make_sprng_seed();
982	+	}
983	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
984	+	#endif
985	+	}
986	+	}//end of if branch of globals->haveSeed()
987	+	else{
988	+
989	+	#ifndef IS_MPI
990	+	seedValue = make_sprng_seed();
991	+	#else
992	+	if (worldRank == 0){
993	+	seedValue = make_sprng_seed();
994	+	}
995	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
996	+	#endif
997	+	}//end of globals->haveSeed()
998	+
999	+	for (int i = 0; i < nInfo; i++){
1000	+	info[i].setSeed(seedValue);
1001	+	}
1002	+
1003	+	#ifdef IS_MPI
1004	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1005	+	MPIcheckPoint();
1006	+	#endif // is_mpi
1007	+	}
1008	+
1009	+
1010	+	void SimSetup::finalInfoCheck(void){
1011	+	int index;
1012	+	int usesDipoles;
1013	+	int usesCharges;
1014	+	int i;
1015	+
1016	+	for (i = 0; i < nInfo; i++){
1017	+	// check electrostatic parameters
1018	+
1019	+	index = 0;
1020	+	usesDipoles = 0;
1021	+	while ((index < info[i].n_atoms) && !usesDipoles){
1022	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1023	+	index++;
1024	+	}
1025	+	index = 0;
1026	+	usesCharges = 0;
1027	+	while ((index < info[i].n_atoms) && !usesCharges){
1028	+	usesCharges= (info[i].atoms[index])->hasCharge();
1029	+	index++;
1030	+	}
1031	+	#ifdef IS_MPI
1032	+	int myUse = usesDipoles;
1033	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1034	+	#endif //is_mpi
1035	+
1036	+	double theRcut, theRsw;
1037	+
1038	+	if (globals->haveRcut()) {
1039	+	theRcut = globals->getRcut();
1040	+
1041	+	if (globals->haveRsw())
1042	+	theRsw = globals->getRsw();
1043	+	else
1044	+	theRsw = theRcut;
1045	+
1046	+	info[i].setDefaultRcut(theRcut, theRsw);
1047	+
1048	+	} else {
1049	+
1050	+	the_ff->calcRcut();
1051	+	theRcut = info[i].getRcut();
1052	+
1053	+	if (globals->haveRsw())
1054	+	theRsw = globals->getRsw();
1055	+	else
1056	+	theRsw = theRcut;
1057	+
1058	+	info[i].setDefaultRcut(theRcut, theRsw);
1059	+	}
1060	+
1061	+	if (globals->getUseRF()){
1062	+	info[i].useReactionField = 1;
1063	+
1064	+	if (!globals->haveRcut()){
1065	+	sprintf(painCave.errMsg,
1066	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067	+	"\tOOPSE will use a default value of 15.0 angstroms"
1068	+	"\tfor the cutoffRadius.\n");
1069	+	painCave.isFatal = 0;
1070	+	simError();
1071	+	theRcut = 15.0;
1072	+	}
1073	+	else{
1074	+	theRcut = globals->getRcut();
1075	+	}
1076	+
1077	+	if (!globals->haveRsw()){
1078	+	sprintf(painCave.errMsg,
1079	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1080	+	"\tOOPSE will use a default value of\n"
1081	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082	+	painCave.isFatal = 0;
1083	+	simError();
1084	+	theRsw = 0.95 * theRcut;
1085	+	}
1086	+	else{
1087	+	theRsw = globals->getRsw();
1088	+	}
1089	+
1090	+	info[i].setDefaultRcut(theRcut, theRsw);
1091	+
1092	+	if (!globals->haveDielectric()){
1093	+	sprintf(painCave.errMsg,
1094	+	"SimSetup Error: No Dielectric constant was set.\n"
1095	+	"\tYou are trying to use Reaction Field without"
1096	+	"\tsetting a dielectric constant!\n");
1097	+	painCave.isFatal = 1;
1098	+	simError();
1099	+	}
1100	+	info[i].dielectric = globals->getDielectric();
1101	+	}
1102	+	else{
1103	+	if (usesDipoles || usesCharges){
1104	+
1105	+	if (!globals->haveRcut()){
1106	+	sprintf(painCave.errMsg,
1107	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1108	+	"\tOOPSE will use a default value of 15.0 angstroms"
1109	+	"\tfor the cutoffRadius.\n");
1110	+	painCave.isFatal = 0;
1111	+	simError();
1112	+	theRcut = 15.0;
1113	+	}
1114	+	else{
1115	+	theRcut = globals->getRcut();
1116	+	}
1117	+
1118	+	if (!globals->haveRsw()){
1119	+	sprintf(painCave.errMsg,
1120	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1121	+	"\tOOPSE will use a default value of\n"
1122	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1123	+	painCave.isFatal = 0;
1124	+	simError();
1125	+	theRsw = 0.95 * theRcut;
1126	+	}
1127	+	else{
1128	+	theRsw = globals->getRsw();
1129	+	}
1130	+
1131	+	info[i].setDefaultRcut(theRcut, theRsw);
1132	+
1133	+	}
1134	+	}
1135		}
1136	+	#ifdef IS_MPI
1137	+	strcpy(checkPointMsg, "post processing checks out");
1138	+	MPIcheckPoint();
1139	+	#endif // is_mpi
1140
1141	<	current_mol++;
1142	<	current_comp_mol++;
1141	>	// clean up the forcefield
1142	>	the_ff->cleanMe();
1143	>	}
1144	>
1145	>	void SimSetup::initSystemCoords(void){
1146	>	int i;
1147
1148	<	if( current_comp_mol >= components_nmol[current_comp] ){
1148	>	char* inName;
1149
1150	<	current_comp_mol = 0;
1151	<	current_comp++;
1150	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1151	>
1152	>	for (i = 0; i < info[0].n_atoms; i++)
1153	>	info[0].atoms[i]->setCoords();
1154	>
1155	>	if (globals->haveInitialConfig()){
1156	>	InitializeFromFile* fileInit;
1157	>	#ifdef IS_MPI // is_mpi
1158	>	if (worldRank == 0){
1159	>	#endif //is_mpi
1160	>	inName = globals->getInitialConfig();
1161	>	fileInit = new InitializeFromFile(inName);
1162	>	#ifdef IS_MPI
1163	>	}
1164	>	else
1165	>	fileInit = new InitializeFromFile(NULL);
1166	>	#endif
1167	>	fileInit->readInit(info); // default velocities on
1168	>
1169	>	delete fileInit;
1170	>	}
1171	>	else{
1172	>
1173	>	// no init from bass
1174	>
1175	>	sprintf(painCave.errMsg,
1176	>	"Cannot intialize a simulation without an initial configuration file.\n");
1177	>	painCave.isFatal = 1;;
1178	>	simError();
1179	>
1180	>	}
1181	>
1182	>	#ifdef IS_MPI
1183	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1184	>	MPIcheckPoint();
1185	>	#endif // is_mpi
1186	>	}
1187	>
1188	>
1189	>	void SimSetup::makeOutNames(void){
1190	>	int k;
1191	>
1192	>
1193	>	for (k = 0; k < nInfo; k++){
1194	>	#ifdef IS_MPI
1195	>	if (worldRank == 0){
1196	>	#endif // is_mpi
1197	>
1198	>	if (globals->haveFinalConfig()){
1199	>	strcpy(info[k].finalName, globals->getFinalConfig());
1200	>	}
1201	>	else{
1202	>	strcpy(info[k].finalName, inFileName);
1203	>	char* endTest;
1204	>	int nameLength = strlen(info[k].finalName);
1205	>	endTest = &(info[k].finalName[nameLength - 5]);
1206	>	if (!strcmp(endTest, ".bass")){
1207	>	strcpy(endTest, ".eor");
1208	>	}
1209	>	else if (!strcmp(endTest, ".BASS")){
1210	>	strcpy(endTest, ".eor");
1211	>	}
1212	>	else{
1213	>	endTest = &(info[k].finalName[nameLength - 4]);
1214	>	if (!strcmp(endTest, ".bss")){
1215	>	strcpy(endTest, ".eor");
1216	>	}
1217	>	else if (!strcmp(endTest, ".mdl")){
1218	>	strcpy(endTest, ".eor");
1219	>	}
1220	>	else{
1221	>	strcat(info[k].finalName, ".eor");
1222	>	}
1223	>	}
1224	>	}
1225	>
1226	>	// make the sample and status out names
1227	>
1228	>	strcpy(info[k].sampleName, inFileName);
1229	>	char* endTest;
1230	>	int nameLength = strlen(info[k].sampleName);
1231	>	endTest = &(info[k].sampleName[nameLength - 5]);
1232	>	if (!strcmp(endTest, ".bass")){
1233	>	strcpy(endTest, ".dump");
1234	>	}
1235	>	else if (!strcmp(endTest, ".BASS")){
1236	>	strcpy(endTest, ".dump");
1237	>	}
1238	>	else{
1239	>	endTest = &(info[k].sampleName[nameLength - 4]);
1240	>	if (!strcmp(endTest, ".bss")){
1241	>	strcpy(endTest, ".dump");
1242	>	}
1243	>	else if (!strcmp(endTest, ".mdl")){
1244	>	strcpy(endTest, ".dump");
1245	>	}
1246	>	else{
1247	>	strcat(info[k].sampleName, ".dump");
1248	>	}
1249	>	}
1250	>
1251	>	strcpy(info[k].statusName, inFileName);
1252	>	nameLength = strlen(info[k].statusName);
1253	>	endTest = &(info[k].statusName[nameLength - 5]);
1254	>	if (!strcmp(endTest, ".bass")){
1255	>	strcpy(endTest, ".stat");
1256	>	}
1257	>	else if (!strcmp(endTest, ".BASS")){
1258	>	strcpy(endTest, ".stat");
1259	>	}
1260	>	else{
1261	>	endTest = &(info[k].statusName[nameLength - 4]);
1262	>	if (!strcmp(endTest, ".bss")){
1263	>	strcpy(endTest, ".stat");
1264	>	}
1265	>	else if (!strcmp(endTest, ".mdl")){
1266	>	strcpy(endTest, ".stat");
1267	>	}
1268	>	else{
1269	>	strcat(info[k].statusName, ".stat");
1270	>	}
1271	>	}
1272	>
1273	>	strcpy(info[k].rawPotName, inFileName);
1274	>	nameLength = strlen(info[k].rawPotName);
1275	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1276	>	if (!strcmp(endTest, ".bass")){
1277	>	strcpy(endTest, ".raw");
1278	>	}
1279	>	else if (!strcmp(endTest, ".BASS")){
1280	>	strcpy(endTest, ".raw");
1281	>	}
1282	>	else{
1283	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1284	>	if (!strcmp(endTest, ".bss")){
1285	>	strcpy(endTest, ".raw");
1286	>	}
1287	>	else if (!strcmp(endTest, ".mdl")){
1288	>	strcpy(endTest, ".raw");
1289	>	}
1290	>	else{
1291	>	strcat(info[k].rawPotName, ".raw");
1292	>	}
1293	>	}
1294	>
1295	>	#ifdef IS_MPI
1296	>
1297	>	}
1298	>	#endif // is_mpi
1299	>	}
1300	>	}
1301	>
1302	>
1303	>	void SimSetup::sysObjectsCreation(void){
1304	>	int i, k;
1305	>
1306	>	// create the forceField
1307	>
1308	>	createFF();
1309	>
1310	>	// extract componentList
1311	>
1312	>	compList();
1313	>
1314	>	// calc the number of atoms, bond, bends, and torsions
1315	>
1316	>	calcSysValues();
1317	>
1318	>	#ifdef IS_MPI
1319	>	// divide the molecules among the processors
1320	>
1321	>	mpiMolDivide();
1322	>	#endif //is_mpi
1323	>
1324	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1325	>
1326	>	makeSysArrays();
1327	>
1328	>	// make and initialize the molecules (all but atomic coordinates)
1329	>
1330	>	makeMolecules();
1331	>
1332	>	for (k = 0; k < nInfo; k++){
1333	>	info[k].identArray = new int[info[k].n_atoms];
1334	>	for (i = 0; i < info[k].n_atoms; i++){
1335	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1336	>	}
1337	>	}
1338	>	}
1339	>
1340	>
1341	>	void SimSetup::createFF(void){
1342	>	switch (ffCase){
1343	>	case FF_DUFF:
1344	>	the_ff = new DUFF();
1345	>	break;
1346	>
1347	>	case FF_LJ:
1348	>	the_ff = new LJFF();
1349	>	break;
1350	>
1351	>	case FF_EAM:
1352	>	the_ff = new EAM_FF();
1353	>	break;
1354	>
1355	>	case FF_H2O:
1356	>	the_ff = new WATER();
1357	>	break;
1358	>
1359	>	default:
1360	>	sprintf(painCave.errMsg,
1361	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1362	>	painCave.isFatal = 1;
1363	>	simError();
1364	>	}
1365	>
1366	>	#ifdef IS_MPI
1367	>	strcpy(checkPointMsg, "ForceField creation successful");
1368	>	MPIcheckPoint();
1369	>	#endif // is_mpi
1370	>	}
1371	>
1372	>
1373	>	void SimSetup::compList(void){
1374	>	int i;
1375	>	char* id;
1376	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1377	>	LinkedMolStamp* currentStamp = NULL;
1378	>	comp_stamps = new MoleculeStamp * [n_components];
1379	>	bool haveCutoffGroups;
1380	>
1381	>	haveCutoffGroups = false;
1382	>
1383	>	// make an array of molecule stamps that match the components used.
1384	>	// also extract the used stamps out into a separate linked list
1385	>
1386	>	for (i = 0; i < nInfo; i++){
1387	>	info[i].nComponents = n_components;
1388	>	info[i].componentsNmol = components_nmol;
1389	>	info[i].compStamps = comp_stamps;
1390	>	info[i].headStamp = headStamp;
1391	>	}
1392	>
1393	>
1394	>	for (i = 0; i < n_components; i++){
1395	>	id = the_components[i]->getType();
1396	>	comp_stamps[i] = NULL;
1397	>
1398	>	// check to make sure the component isn't already in the list
1399	>
1400	>	comp_stamps[i] = headStamp->match(id);
1401	>	if (comp_stamps[i] == NULL){
1402	>	// extract the component from the list;
1403	>
1404	>	currentStamp = stamps->extractMolStamp(id);
1405	>	if (currentStamp == NULL){
1406	>	sprintf(painCave.errMsg,
1407	>	"SimSetup error: Component \"%s\" was not found in the "
1408	>	"list of declared molecules\n",
1409	>	id);
1410	>	painCave.isFatal = 1;
1411	>	simError();
1412	>	}
1413	>
1414	>	headStamp->add(currentStamp);
1415	>	comp_stamps[i] = headStamp->match(id);
1416	>	}
1417	>
1418	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1419	>	haveCutoffGroups = true;
1420	>	}
1421	>
1422	>	for (i = 0; i < nInfo; i++)
1423	>	info[i].haveCutoffGroups = haveCutoffGroups;
1424	>
1425	>	#ifdef IS_MPI
1426	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1427	>	MPIcheckPoint();
1428	>	#endif // is_mpi
1429	>	}
1430	>
1431	>	void SimSetup::calcSysValues(void){
1432	>	int i;
1433	>
1434	>	int* molMembershipArray;
1435	>
1436	>	tot_atoms = 0;
1437	>	tot_bonds = 0;
1438	>	tot_bends = 0;
1439	>	tot_torsions = 0;
1440	>	tot_rigid = 0;
1441	>	for (i = 0; i < n_components; i++){
1442	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1443	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1444	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1445	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1446	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1447	>	}
1448	>
1449	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1450	>	molMembershipArray = new int[tot_atoms];
1451	>
1452	>	for (i = 0; i < nInfo; i++){
1453	>	info[i].n_atoms = tot_atoms;
1454	>	info[i].n_bonds = tot_bonds;
1455	>	info[i].n_bends = tot_bends;
1456	>	info[i].n_torsions = tot_torsions;
1457	>	info[i].n_SRI = tot_SRI;
1458	>	info[i].n_mol = tot_nmol;
1459	>
1460	>	info[i].molMembershipArray = molMembershipArray;
1461	>	}
1462	>	}
1463	>
1464	>	#ifdef IS_MPI
1465	>
1466	>	void SimSetup::mpiMolDivide(void){
1467	>	int i, j, k;
1468	>	int localMol, allMol;
1469	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1470	>	int local_rigid;
1471	>	vector<int> globalMolIndex;
1472	>
1473	>	mpiSim = new mpiSimulation(info);
1474	>
1475	>	mpiSim->divideLabor();
1476	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1477	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1478	>
1479	>	// set up the local variables
1480	>
1481	>	mol2proc = mpiSim->getMolToProcMap();
1482	>	molCompType = mpiSim->getMolComponentType();
1483	>
1484	>	allMol = 0;
1485	>	localMol = 0;
1486	>	local_atoms = 0;
1487	>	local_bonds = 0;
1488	>	local_bends = 0;
1489	>	local_torsions = 0;
1490	>	local_rigid = 0;
1491	>	globalAtomCounter = 0;
1492	>
1493	>	for (i = 0; i < n_components; i++){
1494	>	for (j = 0; j < components_nmol[i]; j++){
1495	>	if (mol2proc[allMol] == worldRank){
1496	>	local_atoms += comp_stamps[i]->getNAtoms();
1497	>	local_bonds += comp_stamps[i]->getNBonds();
1498	>	local_bends += comp_stamps[i]->getNBends();
1499	>	local_torsions += comp_stamps[i]->getNTorsions();
1500	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1501	>	localMol++;
1502	>	}
1503	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1504	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1505	>	globalAtomCounter++;
1506	>	}
1507	>
1508	>	allMol++;
1509	>	}
1510	>	}
1511	>	local_SRI = local_bonds + local_bends + local_torsions;
1512	>
1513	>	info[0].n_atoms = mpiSim->getMyNlocal();
1514	>
1515	>
1516	>	if (local_atoms != info[0].n_atoms){
1517	>	sprintf(painCave.errMsg,
1518	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1519	>	"\tlocalAtom (%d) are not equal.\n",
1520	>	info[0].n_atoms, local_atoms);
1521	>	painCave.isFatal = 1;
1522	>	simError();
1523	>	}
1524	>
1525	>	info[0].n_bonds = local_bonds;
1526	>	info[0].n_bends = local_bends;
1527	>	info[0].n_torsions = local_torsions;
1528	>	info[0].n_SRI = local_SRI;
1529	>	info[0].n_mol = localMol;
1530	>
1531	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1532	>	MPIcheckPoint();
1533	>	}
1534	>
1535	>	#endif // is_mpi
1536	>
1537	>
1538	>	void SimSetup::makeSysArrays(void){
1539	>
1540	>	#ifndef IS_MPI
1541	>	int k, j;
1542	>	#endif // is_mpi
1543	>	int i, l;
1544	>
1545	>	Atom** the_atoms;
1546	>	Molecule* the_molecules;
1547	>
1548	>	for (l = 0; l < nInfo; l++){
1549	>	// create the atom and short range interaction arrays
1550	>
1551	>	the_atoms = new Atom * [info[l].n_atoms];
1552	>	the_molecules = new Molecule[info[l].n_mol];
1553	>	int molIndex;
1554	>
1555	>	// initialize the molecule's stampID's
1556	>
1557	>	#ifdef IS_MPI
1558	>
1559	>
1560	>	molIndex = 0;
1561	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1562	>	if (mol2proc[i] == worldRank){
1563	>	the_molecules[molIndex].setStampID(molCompType[i]);
1564	>	the_molecules[molIndex].setMyIndex(molIndex);
1565	>	the_molecules[molIndex].setGlobalIndex(i);
1566	>	molIndex++;
1567	>	}
1568	>	}
1569	>
1570	>	#else // is_mpi
1571	>
1572	>	molIndex = 0;
1573	>	globalAtomCounter = 0;
1574	>	for (i = 0; i < n_components; i++){
1575	>	for (j = 0; j < components_nmol[i]; j++){
1576	>	the_molecules[molIndex].setStampID(i);
1577	>	the_molecules[molIndex].setMyIndex(molIndex);
1578	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1579	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1580	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1581	>	globalAtomCounter++;
1582	>	}
1583	>	molIndex++;
1584	>	}
1585	>	}
1586	>
1587	>
1588	>	#endif // is_mpi
1589	>
1590	>	info[l].globalExcludes = new int;
1591	>	info[l].globalExcludes[0] = 0;
1592	>
1593	>	// set the arrays into the SimInfo object
1594	>
1595	>	info[l].atoms = the_atoms;
1596	>	info[l].molecules = the_molecules;
1597	>	info[l].nGlobalExcludes = 0;
1598	>
1599	>	the_ff->setSimInfo(info);
1600		}
1601		}
1602	+
1603	+	void SimSetup::makeIntegrator(void){
1604	+	int k;
1605	+
1606	+	NVE<RealIntegrator>* myNVE = NULL;
1607	+	NVT<RealIntegrator>* myNVT = NULL;
1608	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1609	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1610	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1611	+
1612	+	for (k = 0; k < nInfo; k++){
1613	+	switch (ensembleCase){
1614	+	case NVE_ENS:
1615	+	if (globals->haveZconstraints()){
1616	+	setupZConstraint(info[k]);
1617	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1618	+	}
1619	+	else{
1620	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1621	+	}
1622	+
1623	+	info->the_integrator = myNVE;
1624	+	break;
1625	+
1626	+	case NVT_ENS:
1627	+	if (globals->haveZconstraints()){
1628	+	setupZConstraint(info[k]);
1629	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1630	+	}
1631	+	else
1632	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1633	+
1634	+	myNVT->setTargetTemp(globals->getTargetTemp());
1635	+
1636	+	if (globals->haveTauThermostat())
1637	+	myNVT->setTauThermostat(globals->getTauThermostat());
1638	+	else{
1639	+	sprintf(painCave.errMsg,
1640	+	"SimSetup error: If you use the NVT\n"
1641	+	"\tensemble, you must set tauThermostat.\n");
1642	+	painCave.isFatal = 1;
1643	+	simError();
1644	+	}
1645	+
1646	+	info->the_integrator = myNVT;
1647	+	break;
1648	+
1649	+	case NPTi_ENS:
1650	+	if (globals->haveZconstraints()){
1651	+	setupZConstraint(info[k]);
1652	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1653	+	}
1654	+	else
1655	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1656	+
1657	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1658	+
1659	+	if (globals->haveTargetPressure())
1660	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1661	+	else{
1662	+	sprintf(painCave.errMsg,
1663	+	"SimSetup error: If you use a constant pressure\n"
1664	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1665	+	painCave.isFatal = 1;
1666	+	simError();
1667	+	}
1668	+
1669	+	if (globals->haveTauThermostat())
1670	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1671	+	else{
1672	+	sprintf(painCave.errMsg,
1673	+	"SimSetup error: If you use an NPT\n"
1674	+	"\tensemble, you must set tauThermostat.\n");
1675	+	painCave.isFatal = 1;
1676	+	simError();
1677	+	}
1678	+
1679	+	if (globals->haveTauBarostat())
1680	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1681	+	else{
1682	+	sprintf(painCave.errMsg,
1683	+	"SimSetup error: If you use an NPT\n"
1684	+	"\tensemble, you must set tauBarostat.\n");
1685	+	painCave.isFatal = 1;
1686	+	simError();
1687	+	}
1688	+
1689	+	info->the_integrator = myNPTi;
1690	+	break;
1691	+
1692	+	case NPTf_ENS:
1693	+	if (globals->haveZconstraints()){
1694	+	setupZConstraint(info[k]);
1695	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1696	+	}
1697	+	else
1698	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1699	+
1700	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1701	+
1702	+	if (globals->haveTargetPressure())
1703	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1704	+	else{
1705	+	sprintf(painCave.errMsg,
1706	+	"SimSetup error: If you use a constant pressure\n"
1707	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1708	+	painCave.isFatal = 1;
1709	+	simError();
1710	+	}
1711	+
1712	+	if (globals->haveTauThermostat())
1713	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1714	+
1715	+	else{
1716	+	sprintf(painCave.errMsg,
1717	+	"SimSetup error: If you use an NPT\n"
1718	+	"\tensemble, you must set tauThermostat.\n");
1719	+	painCave.isFatal = 1;
1720	+	simError();
1721	+	}
1722	+
1723	+	if (globals->haveTauBarostat())
1724	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1725	+
1726	+	else{
1727	+	sprintf(painCave.errMsg,
1728	+	"SimSetup error: If you use an NPT\n"
1729	+	"\tensemble, you must set tauBarostat.\n");
1730	+	painCave.isFatal = 1;
1731	+	simError();
1732	+	}
1733	+
1734	+	info->the_integrator = myNPTf;
1735	+	break;
1736	+
1737	+	case NPTxyz_ENS:
1738	+	if (globals->haveZconstraints()){
1739	+	setupZConstraint(info[k]);
1740	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1741	+	}
1742	+	else
1743	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1744	+
1745	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1746	+
1747	+	if (globals->haveTargetPressure())
1748	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1749	+	else{
1750	+	sprintf(painCave.errMsg,
1751	+	"SimSetup error: If you use a constant pressure\n"
1752	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1753	+	painCave.isFatal = 1;
1754	+	simError();
1755	+	}
1756	+
1757	+	if (globals->haveTauThermostat())
1758	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1759	+	else{
1760	+	sprintf(painCave.errMsg,
1761	+	"SimSetup error: If you use an NPT\n"
1762	+	"\tensemble, you must set tauThermostat.\n");
1763	+	painCave.isFatal = 1;
1764	+	simError();
1765	+	}
1766	+
1767	+	if (globals->haveTauBarostat())
1768	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1769	+	else{
1770	+	sprintf(painCave.errMsg,
1771	+	"SimSetup error: If you use an NPT\n"
1772	+	"\tensemble, you must set tauBarostat.\n");
1773	+	painCave.isFatal = 1;
1774	+	simError();
1775	+	}
1776	+
1777	+	info->the_integrator = myNPTxyz;
1778	+	break;
1779	+
1780	+	default:
1781	+	sprintf(painCave.errMsg,
1782	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1783	+	painCave.isFatal = 1;
1784	+	simError();
1785	+	}
1786	+	}
1787	+	}
1788	+
1789	+	void SimSetup::initFortran(void){
1790	+	info[0].refreshSim();
1791	+
1792	+	if (!strcmp(info[0].mixingRule, "standard")){
1793	+	the_ff->initForceField(LB_MIXING_RULE);
1794	+	}
1795	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1796	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1797	+	}
1798	+	else{
1799	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1800	+	info[0].mixingRule);
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	}
1804	+
1805	+
1806	+	#ifdef IS_MPI
1807	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1808	+	MPIcheckPoint();
1809	+	#endif // is_mpi
1810	+	}
1811	+
1812	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1813	+	int nZConstraints;
1814	+	ZconStamp** zconStamp;
1815	+
1816	+	if (globals->haveZconstraintTime()){
1817	+	//add sample time of z-constraint  into SimInfo's property list
1818	+	DoubleData* zconsTimeProp = new DoubleData();
1819	+	zconsTimeProp->setID(ZCONSTIME_ID);
1820	+	zconsTimeProp->setData(globals->getZconsTime());
1821	+	theInfo.addProperty(zconsTimeProp);
1822	+	}
1823	+	else{
1824	+	sprintf(painCave.errMsg,
1825	+	"ZConstraint error: If you use a ZConstraint,\n"
1826	+	"\tyou must set zconsTime.\n");
1827	+	painCave.isFatal = 1;
1828	+	simError();
1829	+	}
1830	+
1831	+	//push zconsTol into siminfo, if user does not specify
1832	+	//value for zconsTol, a default value will be used
1833	+	DoubleData* zconsTol = new DoubleData();
1834	+	zconsTol->setID(ZCONSTOL_ID);
1835	+	if (globals->haveZconsTol()){
1836	+	zconsTol->setData(globals->getZconsTol());
1837	+	}
1838	+	else{
1839	+	double defaultZConsTol = 0.01;
1840	+	sprintf(painCave.errMsg,
1841	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1842	+	"\tOOPSE will use a default value of %f.\n"
1843	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1844	+	defaultZConsTol);
1845	+	painCave.isFatal = 0;
1846	+	simError();
1847	+
1848	+	zconsTol->setData(defaultZConsTol);
1849	+	}
1850	+	theInfo.addProperty(zconsTol);
1851	+
1852	+	//set Force Subtraction Policy
1853	+	StringData* zconsForcePolicy = new StringData();
1854	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1855	+
1856	+	if (globals->haveZconsForcePolicy()){
1857	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1858	+	}
1859	+	else{
1860	+	sprintf(painCave.errMsg,
1861	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1862	+	"\tOOPSE will use PolicyByMass.\n"
1863	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1864	+	painCave.isFatal = 0;
1865	+	simError();
1866	+	zconsForcePolicy->setData("BYMASS");
1867	+	}
1868	+
1869	+	theInfo.addProperty(zconsForcePolicy);
1870	+
1871	+	//set zcons gap
1872	+	DoubleData* zconsGap = new DoubleData();
1873	+	zconsGap->setID(ZCONSGAP_ID);
1874	+
1875	+	if (globals->haveZConsGap()){
1876	+	zconsGap->setData(globals->getZconsGap());
1877	+	theInfo.addProperty(zconsGap);
1878	+	}
1879	+
1880	+	//set zcons fixtime
1881	+	DoubleData* zconsFixtime = new DoubleData();
1882	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1883	+
1884	+	if (globals->haveZConsFixTime()){
1885	+	zconsFixtime->setData(globals->getZconsFixtime());
1886	+	theInfo.addProperty(zconsFixtime);
1887	+	}
1888	+
1889	+	//set zconsUsingSMD
1890	+	IntData* zconsUsingSMD = new IntData();
1891	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1892	+
1893	+	if (globals->haveZConsUsingSMD()){
1894	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1895	+	theInfo.addProperty(zconsUsingSMD);
1896	+	}
1897	+
1898	+	//Determine the name of ouput file and add it into SimInfo's property list
1899	+	//Be careful, do not use inFileName, since it is a pointer which
1900	+	//point to a string at master node, and slave nodes do not contain that string
1901	+
1902	+	string zconsOutput(theInfo.finalName);
1903	+
1904	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1905	+
1906	+	StringData* zconsFilename = new StringData();
1907	+	zconsFilename->setID(ZCONSFILENAME_ID);
1908	+	zconsFilename->setData(zconsOutput);
1909	+
1910	+	theInfo.addProperty(zconsFilename);
1911	+
1912	+	//setup index, pos and other parameters of z-constraint molecules
1913	+	nZConstraints = globals->getNzConstraints();
1914	+	theInfo.nZconstraints = nZConstraints;
1915	+
1916	+	zconStamp = globals->getZconStamp();
1917	+	ZConsParaItem tempParaItem;
1918	+
1919	+	ZConsParaData* zconsParaData = new ZConsParaData();
1920	+	zconsParaData->setID(ZCONSPARADATA_ID);
1921	+
1922	+	for (int i = 0; i < nZConstraints; i++){
1923	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1924	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1925	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1926	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1927	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1928	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1929	+	zconsParaData->addItem(tempParaItem);
1930	+	}
1931	+
1932	+	//check the uniqueness of index
1933	+	if(!zconsParaData->isIndexUnique()){
1934	+	sprintf(painCave.errMsg,
1935	+	"ZConstraint Error: molIndex is not unique!\n");
1936	+	painCave.isFatal = 1;
1937	+	simError();
1938	+	}
1939	+
1940	+	//sort the parameters by index of molecules
1941	+	zconsParaData->sortByIndex();
1942	+
1943	+	//push data into siminfo, therefore, we can retrieve later
1944	+	theInfo.addProperty(zconsParaData);
1945	+	}
1946	+
1947	+	void SimSetup::makeMinimizer(){
1948	+
1949	+	OOPSEMinimizer* myOOPSEMinimizer;
1950	+	MinimizerParameterSet* param;
1951	+	char minimizerName[100];
1952	+
1953	+	for (int i = 0; i < nInfo; i++){
1954	+
1955	+	//prepare parameter set for minimizer
1956	+	param = new MinimizerParameterSet();
1957	+	param->setDefaultParameter();
1958	+
1959	+	if (globals->haveMinimizer()){
1960	+	param->setFTol(globals->getMinFTol());
1961	+	}
1962	+
1963	+	if (globals->haveMinGTol()){
1964	+	param->setGTol(globals->getMinGTol());
1965	+	}
1966	+
1967	+	if (globals->haveMinMaxIter()){
1968	+	param->setMaxIteration(globals->getMinMaxIter());
1969	+	}
1970	+
1971	+	if (globals->haveMinWriteFrq()){
1972	+	param->setMaxIteration(globals->getMinMaxIter());
1973	+	}
1974	+
1975	+	if (globals->haveMinWriteFrq()){
1976	+	param->setWriteFrq(globals->getMinWriteFrq());
1977	+	}
1978	+
1979	+	if (globals->haveMinStepSize()){
1980	+	param->setStepSize(globals->getMinStepSize());
1981	+	}
1982	+
1983	+	if (globals->haveMinLSMaxIter()){
1984	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1985	+	}
1986	+
1987	+	if (globals->haveMinLSTol()){
1988	+	param->setLineSearchTol(globals->getMinLSTol());
1989	+	}
1990	+
1991	+	strcpy(minimizerName, globals->getMinimizer());
1992	+
1993	+	if (!strcasecmp(minimizerName, "CG")){
1994	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1995	+	}
1996	+	else if (!strcasecmp(minimizerName, "SD")){
1997	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1998	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1999	+	}
2000	+	else{
2001	+	sprintf(painCave.errMsg,
2002	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2003	+	painCave.isFatal = 0;
2004	+	simError();
2005	+
2006	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2007	+	}
2008	+	info[i].the_integrator = myOOPSEMinimizer;
2009	+
2010	+	//store the minimizer into simInfo
2011	+	info[i].the_minimizer = myOOPSEMinimizer;
2012	+	info[i].has_minimizer = true;
2013	+	}
2014	+
2015	+	}

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