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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 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	<
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145	>	}
146
147	<	// 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];
147	>	// make the output filenames
148
149	<	if( !the_globals->haveNMol() ){
150	<	// we don't have the total number of molecules, so we assume it is
151	<	// given in each component
149	>	makeOutNames();
150	>
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
155	>	// initialize the Fortran
156
157	<	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	<	}
157	>	initFortran();
158
159	<	tot_nmol += the_components[i]->getNMol();
160	<	components_nmol[i] = the_components[i]->getNMol();
161	<	}
162	<	}
163	<	else{
164	<	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	<	}
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
166	>	}
167
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
168
169	<	simnfo->nComponents = n_components;
170	<	simnfo->componentsNmol = components_nmol;
171	<	simnfo->compStamps = comp_stamps;
172	<	simnfo->headStamp = new LinkedMolStamp();
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
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
189	>	bond_pair* theBonds;
190	>	bend_set* theBends;
191	>	torsion_set* theTorsions;
192
193	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
193	>	set<int> skipList;
194
195	<	comp_stamps[i] = headStamp->match( id );
196	<	if( comp_stamps[i] == NULL ){
197	<
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	<	}
195	>	double phi, theta, psi;
196	>	char* molName;
197	>	char rbName[100];
198
199	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
199	>	//init the forceField paramters
200
201	+	the_ff->readParams();
202
203	+	// init the atoms
204
205	<	// caclulate the number of atoms, bonds, bends and torsions
205	>	int nMembers, nNew, rb1, rb2;
206
207	<	tot_atoms = 0;
208	<	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	<	}
207	>	for (k = 0; k < nInfo; k++){
208	>	the_ff->setSimInfo(&(info[k]));
209
210	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
210	>	atomOffset = 0;
211
212	<	simnfo->n_atoms = tot_atoms;
213	<	simnfo->n_bonds = tot_bonds;
214	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
212	>	for (i = 0; i < info[k].n_mol; i++){
213	>	stampID = info[k].molecules[i].getStampID();
214	>	molName = comp_stamps[stampID]->getID();
215
216	<
217	<	#ifdef IS_MPI
216	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
219	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222	>
223	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
224
225	<	// divide the molecules among processors here.
226	<
227	<	mpiSim = new mpiSimulation( simnfo );
228	<
241	<
225	>	if (molInfo.nBonds > 0)
226	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	>	else
228	>	molInfo.myBonds = NULL;
229
230	<	globalIndex = mpiSim->divideLabor();
230	>	if (molInfo.nBends > 0)
231	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	>	else
233	>	molInfo.myBends = NULL;
234
235	+	if (molInfo.nTorsions > 0)
236	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	+	else
238	+	molInfo.myTorsions = NULL;
239
240	<
241	<	// set up the local variables
242	<
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++ ){
240	>	theBonds = new bond_pair[molInfo.nBonds];
241	>	theBends = new bend_set[molInfo.nBends];
242	>	theTorsions = new torsion_set[molInfo.nTorsions];
243
244	<	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	<
244	>	// make the Atoms
245
246	<	simnfo->n_atoms = mpiSim->getMyNlocal();
247	<
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	<	}
246	>	for (j = 0; j < molInfo.nAtoms; j++){
247	>	currentAtom = comp_stamps[stampID]->getAtom(j);
248
249	<	simnfo->n_bonds = local_bonds;
250	<	simnfo->n_bends = local_bends;
251	<	simnfo->n_torsions = local_torsions;
252	<	simnfo->n_SRI = local_SRI;
253	<	simnfo->n_mol = localMol;
249	>	if (currentAtom->haveOrientation()){
250	>	dAtom = new DirectionalAtom((j + atomOffset),
251	>	info[k].getConfiguration());
252	>	info[k].n_oriented++;
253	>	molInfo.myAtoms[j] = dAtom;
254
255	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
256	<	MPIcheckPoint();
257	<
298	<
299	<	#endif // is_mpi
300	<
255	>	// Directional Atoms have standard unit vectors which are oriented
256	>	// in space using the three Euler angles.  We assume the standard
257	>	// unit vector was originally along the z axis below.
258
259	<	// create the atom and short range interaction arrays
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262
263	<	Atom::createArrays(simnfo->n_atoms);
264	<	the_atoms = new Atom*[simnfo->n_atoms];
265	<	the_molecules = new Molecule[simnfo->n_mol];
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267
268	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269
270	<	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;
270	>	}
271
272	<	simnfo->n_exclude = 1;
273	<	}
272	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
273	>	#ifdef IS_MPI
274
275	<	// set the arrays into the SimInfo object
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
328	–	simnfo->atoms = the_atoms;
329	–	simnfo->sr_interactions = the_sris;
330	–	simnfo->nGlobalExcludes = 0;
331	–	simnfo->excludes = the_excludes;
332	–
333	–
334	–	// get some of the tricky things that may still be in the globals
335	–
336	–	if( simnfo->n_dipoles ){
337	–
338	–	if( !the_globals->haveRRF() ){
339	–	sprintf( painCave.errMsg,
340	–	"SimSetup Error, system has dipoles, but no rRF was set.\n");
341	–	painCave.isFatal = 1;
342	–	simError();
343	–	}
344	–	if( !the_globals->haveDielectric() ){
345	–	sprintf( painCave.errMsg,
346	–	"SimSetup Error, system has dipoles, but no"
347	–	" dielectric was set.\n" );
348	–	painCave.isFatal = 1;
349	–	simError();
350	–	}
351	–
352	–	simnfo->rRF        = the_globals->getRRF();
353	–	simnfo->dielectric = the_globals->getDielectric();
354	–	}
355	–
356	–	#ifdef IS_MPI
357	–	strcpy( checkPointMsg, "rRf and dielectric check out" );
358	–	MPIcheckPoint();
277		#endif // is_mpi
278	<
361	<	if( the_globals->haveBox() ){
362	<	simnfo->box_x = the_globals->getBox();
363	<	simnfo->box_y = the_globals->getBox();
364	<	simnfo->box_z = the_globals->getBox();
365	<	}
366	<	else if( the_globals->haveDensity() ){
278	>	}
279
280	<	double vol;
281	<	vol = (double)tot_nmol / the_globals->getDensity();
282	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
283	<	simnfo->box_y = simnfo->box_x;
284	<	simnfo->box_z = simnfo->box_x;
373	<	}
374	<	else{
375	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285
286	<	if( !the_globals->haveBoxY() ){
287	<	sprintf( painCave.errMsg,
385	<	"SimSetup error, no periodic BoxY size given.\n" );
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<	simnfo->box_y = the_globals->getBoxY();
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288
391	–	if( !the_globals->haveBoxZ() ){
392	–	sprintf( painCave.errMsg,
393	–	"SimSetup error, no periodic BoxZ size given.\n" );
394	–	painCave.isFatal = 1;
395	–	simError();
396	–	}
397	–	simnfo->box_z = the_globals->getBoxZ();
398	–	}
399	–
289		#ifdef IS_MPI
290	<	strcpy( checkPointMsg, "Box size set up" );
291	<	MPIcheckPoint();
292	<	#endif // is_mpi
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	+	info[k].excludes->addPair(exI, exJ);
298	+	}
299
300	<	// initialize the arrays
300	>	//make the bends
301	>	for (j = 0; j < molInfo.nBends; j++){
302	>	currentBend = comp_stamps[stampID]->getBend(j);
303	>	theBends[j].a = currentBend->getA() + atomOffset;
304	>	theBends[j].b = currentBend->getB() + atomOffset;
305	>	theBends[j].c = currentBend->getC() + atomOffset;
306
307	<	the_ff->setSimInfo( simnfo );
307	>	if (currentBend->haveExtras()){
308	>	extras = currentBend->getExtras();
309	>	current_extra = extras;
310
311	<	makeAtoms();
312	<	simnfo->identArray = new int[simnfo->n_atoms];
313	<	for(i=0; i<simnfo->n_atoms; i++){
314	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
315	<	}
316	<
317	<	if( tot_bonds ){
417	<	makeBonds();
418	<	}
419	<
420	<	if( tot_bends ){
421	<	makeBends();
422	<	}
423	<
424	<	if( tot_torsions ){
425	<	makeTorsions();
426	<	}
427	<
311	>	while (current_extra != NULL){
312	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
313	>	switch (current_extra->getType()){
314	>	case 0:
315	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
316	>	theBends[j].isGhost = 1;
317	>	break;
318
319	+	case 1:
320	+	theBends[j].ghost = (int) current_extra->getDouble() +
321	+	atomOffset;
322	+	theBends[j].isGhost = 1;
323	+	break;
324
325	+	default:
326	+	sprintf(painCave.errMsg,
327	+	"SimSetup Error: ghostVectorSource was neither a "
328	+	"double nor an int.\n"
329	+	"-->Bend[%d] in %s\n",
330	+	j, comp_stamps[stampID]->getID());
331	+	painCave.isFatal = 1;
332	+	simError();
333	+	}
334	+	}
335	+	else{
336	+	sprintf(painCave.errMsg,
337	+	"SimSetup Error: unhandled bend assignment:\n"
338	+	"    -->%s in Bend[%d] in %s\n",
339	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
340	+	painCave.isFatal = 1;
341	+	simError();
342	+	}
343
344	+	current_extra = current_extra->getNext();
345	+	}
346	+	}
347
348	+	if (theBends[j].isGhost) {
349	+
350	+	tempI = theBends[j].a;
351	+	tempJ = theBends[j].b;
352	+
353	+	#ifdef IS_MPI
354	+	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	+	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	+	#else
357	+	exI = tempI + 1;
358	+	exJ = tempJ + 1;
359	+	#endif
360	+	info[k].excludes->addPair(exI, exJ);
361
362	<	if( the_globals->haveInitialConfig() ){
363	<
364	<	InitializeFromFile* fileInit;
365	<	#ifdef IS_MPI // is_mpi
366	<	if( worldRank == 0 ){
367	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
362	>	} else {
363	>
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368		#ifdef IS_MPI
369	<	}else fileInit = new InitializeFromFile( NULL );
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376		#endif
377	<	fileInit->read_xyz( simnfo ); // default velocities on
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382	>	}
383
384	<	delete fileInit;
385	<	}
386	<	else{
384	>	for (j = 0; j < molInfo.nTorsions; j++){
385	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
386	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
387	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
388	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
389	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	<	#ifdef IS_MPI
391	>	tempI = theTorsions[j].a;
392	>	tempJ = theTorsions[j].b;
393	>	tempK = theTorsions[j].c;
394	>	tempL = theTorsions[j].d;
395
396	<	// no init from bass
397	<
398	<	sprintf( painCave.errMsg,
399	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
400	<	painCave.isFatal;
456	<	simError();
457	<
396	>	#ifdef IS_MPI
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401		#else
402	+	exI = tempI + 1;
403	+	exJ = tempJ + 1;
404	+	exK = tempK + 1;
405	+	exL = tempL + 1;
406	+	#endif
407
408	<	initFromBass();
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415
416	+
417	+	molInfo.myRigidBodies.clear();
418	+
419	+	for (j = 0; j < molInfo.nRigidBodies; j++){
420
421	<	#endif
422	<	}
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423
424	<	#ifdef IS_MPI
467	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
468	<	MPIcheckPoint();
469	<	#endif // is_mpi
424	>	// Create the Rigid Body:
425
426	+	myRB = new RigidBody();
427
428	<
429	<
430	<
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432
433	<
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435	>
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438	>
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442	>
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445	>
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449		#ifdef IS_MPI
450	<	if( worldRank == 0 ){
451	<	#endif // is_mpi
452	<
453	<	if( the_globals->haveFinalConfig() ){
454	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
455	<	}
456	<	else{
457	<	strcpy( simnfo->finalName, inFileName );
458	<	char* endTest;
459	<	int nameLength = strlen( simnfo->finalName );
460	<	endTest = &(simnfo->finalName[nameLength - 5]);
461	<	if( !strcmp( endTest, ".bass" ) ){
462	<	strcpy( endTest, ".eor" );
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469	>	#ifdef IS_MPI
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481	>
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484		}
485	<	else if( !strcmp( endTest, ".BASS" ) ){
486	<	strcpy( endTest, ".eor" );
487	<	}
488	<	else{
489	<	endTest = &(simnfo->finalName[nameLength - 4]);
490	<	if( !strcmp( endTest, ".bss" ) ){
491	<	strcpy( endTest, ".eor" );
492	<	}
493	<	else if( !strcmp( endTest, ".mdl" ) ){
494	<	strcpy( endTest, ".eor" );
495	<	}
496	<	else{
497	<	strcat( simnfo->finalName, ".eor" );
498	<	}
499	<	}
500	<	}
501	<
502	<	// make the sample and status out names
503	<
504	<	strcpy( simnfo->sampleName, inFileName );
505	<	char* endTest;
506	<	int nameLength = strlen( simnfo->sampleName );
507	<	endTest = &(simnfo->sampleName[nameLength - 5]);
508	<	if( !strcmp( endTest, ".bass" ) ){
509	<	strcpy( endTest, ".dump" );
510	<	}
511	<	else if( !strcmp( endTest, ".BASS" ) ){
512	<	strcpy( endTest, ".dump" );
513	<	}
514	<	else{
515	<	endTest = &(simnfo->sampleName[nameLength - 4]);
516	<	if( !strcmp( endTest, ".bss" ) ){
517	<	strcpy( endTest, ".dump" );
518	<	}
519	<	else if( !strcmp( endTest, ".mdl" ) ){
520	<	strcpy( endTest, ".dump" );
521	<	}
522	<	else{
523	<	strcat( simnfo->sampleName, ".dump" );
524	<	}
525	<	}
526	<
527	<	strcpy( simnfo->statusName, inFileName );
528	<	nameLength = strlen( simnfo->statusName );
529	<	endTest = &(simnfo->statusName[nameLength - 5]);
530	<	if( !strcmp( endTest, ".bass" ) ){
531	<	strcpy( endTest, ".stat" );
532	<	}
540	<	else if( !strcmp( endTest, ".BASS" ) ){
541	<	strcpy( endTest, ".stat" );
542	<	}
543	<	else{
544	<	endTest = &(simnfo->statusName[nameLength - 4]);
545	<	if( !strcmp( endTest, ".bss" ) ){
546	<	strcpy( endTest, ".stat" );
547	<	}
548	<	else if( !strcmp( endTest, ".mdl" ) ){
549	<	strcpy( endTest, ".stat" );
485	>
486	>
487	>	//create cutoff group for molecule
488	>	molInfo.myCutoffGroups.clear();
489	>	for (j = 0; j < molInfo.nCutoffGroups; j++){
490	>
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493	>
494	>	myCutoffGroup = new CutoffGroup();
495	>
496	>	for (int cg = 0; cg < nMembers; cg++) {
497	>
498	>	// molI is atom numbering inside this molecule
499	>	molI = currentCutoffGroup->getMember(cg);
500	>
501	>	// tempI is atom numbering on local processor
502	>	tempI = molI + atomOffset;
503	>
504	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	>	}
506	>
507	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	>
510	>
511	>
512	>	// After this is all set up, scan through the atoms to
513	>	// see if they can be added to the integrableObjects:
514	>
515	>	molInfo.myIntegrableObjects.clear();
516	>
517	>
518	>	for (j = 0; j < molInfo.nAtoms; j++){
519	>
520	>	#ifdef IS_MPI
521	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	>	#else
523	>	slJ = j+atomOffset;
524	>	#endif
525	>
526	>	// if they aren't on the skip list, then they can be integrated
527	>
528	>	if (skipList.find(slJ) == skipList.end()) {
529	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	>	info[k].integrableObjects.push_back(mySD);
531	>	molInfo.myIntegrableObjects.push_back(mySD);
532	>	}
533		}
534	<	else{
535	<	strcat( simnfo->statusName, ".stat" );
534	>
535	>	// all rigid bodies are integrated:
536	>
537	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	>	info[k].integrableObjects.push_back(mySD);
540	>	molInfo.myIntegrableObjects.push_back(mySD);
541		}
554	–	}
542
543	<	#ifdef IS_MPI
544	<	}
545	<	#endif // is_mpi
546	<
547	<	// set the status, sample, and themal kick times
548	<
549	<	if( the_globals->haveSampleTime() ){
550	<	simnfo->sampleTime = the_globals->getSampleTime();
564	<	simnfo->statusTime = simnfo->sampleTime;
565	<	simnfo->thermalTime = simnfo->sampleTime;
566	<	}
567	<	else{
568	<	simnfo->sampleTime = the_globals->getRunTime();
569	<	simnfo->statusTime = simnfo->sampleTime;
570	<	simnfo->thermalTime = simnfo->sampleTime;
571	<	}
543	>
544	>	// send the arrays off to the forceField for init.
545	>
546	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550	>	theTorsions);
551
552	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
552	>	info[k].molecules[i].initialize(molInfo);
553
554	<	if( the_globals->haveThermalTime() ){
555	<	simnfo->thermalTime = the_globals->getThermalTime();
554	>
555	>	atomOffset += molInfo.nAtoms;
556	>	delete[] theBonds;
557	>	delete[] theBends;
558	>	delete[] theTorsions;
559	>	}
560		}
561
562	<	// check for the temperature set flag
562	>	#ifdef IS_MPI
563	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
564	>	MPIcheckPoint();
565	>	#endif // is_mpi
566
567	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
567	>	}
568
569	+	void SimSetup::initFromBass(void){
570	+	int i, j, k;
571	+	int n_cells;
572	+	double cellx, celly, cellz;
573	+	double temp1, temp2, temp3;
574	+	int n_per_extra;
575	+	int n_extra;
576	+	int have_extra, done;
577
578	<	//   // make the longe range forces and the integrator
578	>	double vel[3];
579	>	vel[0] = 0.0;
580	>	vel[1] = 0.0;
581	>	vel[2] = 0.0;
582
583	<	//   new AllLong( simnfo );
583	>	temp1 = (double) tot_nmol / 4.0;
584	>	temp2 = pow(temp1, (1.0 / 3.0));
585	>	temp3 = ceil(temp2);
586
587	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
588	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
589	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
590	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
587	>	have_extra = 0;
588	>	if (temp2 < temp3){
589	>	// we have a non-complete lattice
590	>	have_extra = 1;
591
592	+	n_cells = (int) temp3 - 1;
593	+	cellx = info[0].boxL[0] / temp3;
594	+	celly = info[0].boxL[1] / temp3;
595	+	cellz = info[0].boxL[2] / temp3;
596	+	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
597	+	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
598	+	n_per_extra = (int) ceil(temp1);
599
600	<
601	<	// initialize the Fortran
602	<
603	<	simnfo->refreshSim();
604	<
605	<	if( !strcmp( simnfo->mixingRule, "standard") ){
606	<	the_ff->initForceField( LB_MIXING_RULE );
600	>	if (n_per_extra > 4){
601	>	sprintf(painCave.errMsg,
602	>	"SimSetup error. There has been an error in constructing"
603	>	" the non-complete lattice.\n");
604	>	painCave.isFatal = 1;
605	>	simError();
606	>	}
607		}
604	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
605	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
606	–	}
608		else{
609	<	sprintf( painCave.errMsg,
610	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
611	<	simnfo->mixingRule );
612	<	painCave.isFatal = 1;
612	<	simError();
609	>	n_cells = (int) temp3;
610	>	cellx = info[0].boxL[0] / temp3;
611	>	celly = info[0].boxL[1] / temp3;
612	>	cellz = info[0].boxL[2] / temp3;
613		}
614
615	+	current_mol = 0;
616	+	current_comp_mol = 0;
617	+	current_comp = 0;
618	+	current_atom_ndx = 0;
619
620	<	#ifdef IS_MPI
621	<	strcpy( checkPointMsg,
622	<	"Successfully intialized the mixingRule for Fortran." );
623	<	MPIcheckPoint();
620	<	#endif // is_mpi
621	<	}
620	>	for (i = 0; i < n_cells ; i++){
621	>	for (j = 0; j < n_cells; j++){
622	>	for (k = 0; k < n_cells; k++){
623	>	makeElement(i * cellx, j * celly, k * cellz);
624
625	<	void SimSetup::makeAtoms( void ){
625	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
626
627	<	int i, j, k, index;
626	<	double ux, uy, uz, uSqr, u;
627	<	AtomStamp* current_atom;
627	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
628
629	<	DirectionalAtom* dAtom;
630	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
629	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
630	>	}
631	>	}
632	>	}
633
634	<	lMolIndex = 0;
635	<	molIndex = 0;
634	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
634	>	if (have_extra){
635	>	done = 0;
636
637	<	for( j=0; j<components_nmol[i]; j++ ){
637	>	int start_ndx;
638	>	for (i = 0; i < (n_cells + 1) && !done; i++){
639	>	for (j = 0; j < (n_cells + 1) && !done; j++){
640	>	if (i < n_cells){
641	>	if (j < n_cells){
642	>	start_ndx = n_cells;
643	>	}
644	>	else
645	>	start_ndx = 0;
646	>	}
647	>	else
648	>	start_ndx = 0;
649
650	<	#ifdef IS_MPI
651	<	if( mpiSim->getMyMolStart() <= molIndex &&
652	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
650	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
651	>	makeElement(i * cellx, j * celly, k * cellz);
652	>	done = (current_mol >= tot_nmol);
653
654	<	molStart = index;
655	<	nMemb = comp_stamps[i]->getNAtoms();
656	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
657	<
658	<	current_atom = comp_stamps[i]->getAtom( k );
659	<	if( current_atom->haveOrientation() ){
660	<
661	<	dAtom = new DirectionalAtom(index);
662	<	simnfo->n_oriented++;
663	<	the_atoms[index] = dAtom;
664	<
665	<	ux = current_atom->getOrntX();
666	<	uy = current_atom->getOrntY();
667	<	uz = current_atom->getOrntZ();
668	<
669	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
670	<
671	<	u = sqrt( uSqr );
672	<	ux = ux / u;
673	<	uy = uy / u;
674	<	uz = uz / u;
675	<
676	<	dAtom->setSUx( ux );
677	<	dAtom->setSUy( uy );
678	<	dAtom->setSUz( uz );
679	<	}
680	<	else{
681	<	the_atoms[index] = new GeneralAtom(index);
682	<	}
683	<	the_atoms[index]->setType( current_atom->getType() );
684	<	the_atoms[index]->setIndex( index );
685	<
686	<	// increment the index and repeat;
687	<	index++;
688	<	}
689	<
690	<	molEnd = index -1;
691	<	the_molecules[lMolIndex].setNMembers( nMemb );
692	<	the_molecules[lMolIndex].setStartAtom( molStart );
693	<	the_molecules[lMolIndex].setEndAtom( molEnd );
694	<	the_molecules[lMolIndex].setStampID( i );
695	<	lMolIndex++;
696	<
697	<	#ifdef IS_MPI
698	<	}
689	<	#endif //is_mpi
690	<
691	<	molIndex++;
654	>	if (!done && n_per_extra > 1){
655	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
656	>	k * cellz);
657	>	done = (current_mol >= tot_nmol);
658	>	}
659	>
660	>	if (!done && n_per_extra > 2){
661	>	makeElement(i * cellx, j * celly + 0.5 * celly,
662	>	k * cellz + 0.5 * cellz);
663	>	done = (current_mol >= tot_nmol);
664	>	}
665	>
666	>	if (!done && n_per_extra > 3){
667	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
668	>	k * cellz + 0.5 * cellz);
669	>	done = (current_mol >= tot_nmol);
670	>	}
671	>	}
672	>	}
673	>	}
674	>	}
675	>
676	>	for (i = 0; i < info[0].n_atoms; i++){
677	>	info[0].atoms[i]->setVel(vel);
678	>	}
679	>	}
680	>
681	>	void SimSetup::makeElement(double x, double y, double z){
682	>	int k;
683	>	AtomStamp* current_atom;
684	>	DirectionalAtom* dAtom;
685	>	double rotMat[3][3];
686	>	double pos[3];
687	>
688	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
689	>	current_atom = comp_stamps[current_comp]->getAtom(k);
690	>	if (!current_atom->havePosition()){
691	>	sprintf(painCave.errMsg,
692	>	"SimSetup:initFromBass error.\n"
693	>	"\tComponent %s, atom %s does not have a position specified.\n"
694	>	"\tThe initialization routine is unable to give a start"
695	>	" position.\n",
696	>	comp_stamps[current_comp]->getID(), current_atom->getType());
697	>	painCave.isFatal = 1;
698	>	simError();
699		}
693	–	}
700
701	<	#ifdef IS_MPI
702	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
703	<
698	<	delete[] globalIndex;
701	>	pos[0] = x + current_atom->getPosX();
702	>	pos[1] = y + current_atom->getPosY();
703	>	pos[2] = z + current_atom->getPosZ();
704
705	<	mpiSim->mpiRefresh();
701	<	#endif //IS_MPI
702	<
703	<	the_ff->initializeAtoms();
704	<	}
705	>	info[0].atoms[current_atom_ndx]->setPos(pos);
706
707	<	void SimSetup::makeBonds( void ){
707	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
708	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
709
710	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
711	<	bond_pair* the_bonds;
712	<	BondStamp* current_bond;
710	>	rotMat[0][0] = 1.0;
711	>	rotMat[0][1] = 0.0;
712	>	rotMat[0][2] = 0.0;
713
714	<	the_bonds = new bond_pair[tot_bonds];
715	<	index = 0;
716	<	offset = 0;
715	<	molIndex = 0;
714	>	rotMat[1][0] = 0.0;
715	>	rotMat[1][1] = 1.0;
716	>	rotMat[1][2] = 0.0;
717
718	<	for( i=0; i<n_components; i++ ){
718	>	rotMat[2][0] = 0.0;
719	>	rotMat[2][1] = 0.0;
720	>	rotMat[2][2] = 1.0;
721
722	<	for( j=0; j<components_nmol[i]; j++ ){
722	>	dAtom->setA(rotMat);
723	>	}
724
725	<	#ifdef IS_MPI
726	<	if( mpiSim->getMyMolStart() <= molIndex &&
723	<	molIndex <= mpiSim->getMyMolEnd() ){
724	<	#endif // is_mpi
725	<
726	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727	<
728	<	current_bond = comp_stamps[i]->getBond( k );
729	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
725	>	current_atom_ndx++;
726	>	}
727
728	<	exI = the_bonds[index].a;
729	<	exJ = the_bonds[index].b;
728	>	current_mol++;
729	>	current_comp_mol++;
730
731	<	// exclude_I must always be the smaller of the pair
732	<	if( exI > exJ ){
733	<	tempEx = exI;
734	<	exI = exJ;
735	<	exJ = tempEx;
740	<	}
731	>	if (current_comp_mol >= components_nmol[current_comp]){
732	>	current_comp_mol = 0;
733	>	current_comp++;
734	>	}
735	>	}
736
742	–
743	–	#ifdef IS_MPI
737
738	<	the_excludes[index*2] =
739	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
738	>	void SimSetup::gatherInfo(void){
739	>	int i;
740
741	<	#else  // isn't MPI
742	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
763	<	}
764	<	#endif //is_mpi
765	<
766	<	molIndex++;
767	<	}
768	<	}
741	>	ensembleCase = -1;
742	>	ffCase = -1;
743
744	<	the_ff->initializeBonds( the_bonds );
771	<	}
744	>	// set the easy ones first
745
746	<	void SimSetup::makeBends( void ){
746	>	for (i = 0; i < nInfo; i++){
747	>	info[i].target_temp = globals->getTargetTemp();
748	>	info[i].dt = globals->getDt();
749	>	info[i].run_time = globals->getRunTime();
750	>	}
751	>	n_components = globals->getNComponents();
752
775	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
776	–	bend_set* the_bends;
777	–	BendStamp* current_bend;
778	–	LinkedAssign* extras;
779	–	LinkedAssign* current_extra;
780	–
753
754	<	the_bends = new bend_set[tot_bends];
783	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
786	<	for( i=0; i<n_components; i++ ){
754	>	// get the forceField
755
756	<	for( j=0; j<components_nmol[i]; j++ ){
756	>	strcpy(force_field, globals->getForceField());
757
758	<	#ifdef IS_MPI
759	<	if( mpiSim->getMyMolStart() <= molIndex &&
760	<	molIndex <= mpiSim->getMyMolEnd() ){
761	<	#endif // is_mpi
758	>	if (!strcasecmp(force_field, "DUFF")){
759	>	ffCase = FF_DUFF;
760	>	}
761	>	else if (!strcasecmp(force_field, "LJ")){
762	>	ffCase = FF_LJ;
763	>	}
764	>	else if (!strcasecmp(force_field, "EAM")){
765	>	ffCase = FF_EAM;
766	>	}
767	>	else if (!strcasecmp(force_field, "WATER")){
768	>	ffCase = FF_H2O;
769	>	}
770	>	else{
771	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
772	>	force_field);
773	>	painCave.isFatal = 1;
774	>	simError();
775	>	}
776
777	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
777	>	// get the ensemble
778
779	+	strcpy(ensemble, globals->getEnsemble());
780
781	<	#ifdef IS_MPI
781	>	if (!strcasecmp(ensemble, "NVE")){
782	>	ensembleCase = NVE_ENS;
783	>	}
784	>	else if (!strcasecmp(ensemble, "NVT")){
785	>	ensembleCase = NVT_ENS;
786	>	}
787	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
788	>	ensembleCase = NPTi_ENS;
789	>	}
790	>	else if (!strcasecmp(ensemble, "NPTf")){
791	>	ensembleCase = NPTf_ENS;
792	>	}
793	>	else if (!strcasecmp(ensemble, "NPTxyz")){
794	>	ensembleCase = NPTxyz_ENS;
795	>	}
796	>	else{
797	>	sprintf(painCave.errMsg,
798	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
799	>	"\treverting to NVE for this simulation.\n",
800	>	ensemble);
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	strcpy(ensemble, "NVE");
804	>	ensembleCase = NVE_ENS;
805	>	}
806
807	<	the_excludes[(index + tot_bonds)*2] =
808	<	the_atoms[exI]->getGlobalIndex() + 1;
873	<	the_excludes[(index + tot_bonds)*2 + 1] =
874	<	the_atoms[exJ]->getGlobalIndex() + 1;
875	<
876	<	#else  // isn't MPI
877	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
881	<	#endif  //is_mpi
882	<
883	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
890	<	}
891	<	#endif //is_mpi
807	>	for (i = 0; i < nInfo; i++){
808	>	strcpy(info[i].ensemble, ensemble);
809
810	<	molIndex++;
811	<	}
810	>	// get the mixing rule
811	>
812	>	strcpy(info[i].mixingRule, globals->getMixingRule());
813	>	info[i].usePBC = globals->getPBC();
814		}
815
816	<	#ifdef IS_MPI
898	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
900	<	MPIcheckPoint();
901	<	#endif // is_mpi
902	<
816	>	// get the components and calculate the tot_nMol and indvidual n_mol
817
818	<	the_ff->initializeBends( the_bends );
819	<	}
818	>	the_components = globals->getComponents();
819	>	components_nmol = new int[n_components];
820
907	–	void SimSetup::makeTorsions( void ){
821
822	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
823	<	torsion_set* the_torsions;
824	<	TorsionStamp* current_torsion;
822	>	if (!globals->haveNMol()){
823	>	// we don't have the total number of molecules, so we assume it is
824	>	// given in each component
825
826	<	the_torsions = new torsion_set[tot_torsions];
827	<	index = 0;
828	<	offset = 0;
829	<	molIndex = 0;
830	<	for( i=0; i<n_components; i++ ){
826	>	tot_nmol = 0;
827	>	for (i = 0; i < n_components; i++){
828	>	if (!the_components[i]->haveNMol()){
829	>	// we have a problem
830	>	sprintf(painCave.errMsg,
831	>	"SimSetup Error. No global NMol or component NMol given.\n"
832	>	"\tCannot calculate the number of atoms.\n");
833	>	painCave.isFatal = 1;
834	>	simError();
835	>	}
836
837	<	for( j=0; j<components_nmol[i]; j++ ){
837	>	tot_nmol += the_components[i]->getNMol();
838	>	components_nmol[i] = the_components[i]->getNMol();
839	>	}
840	>	}
841	>	else{
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup error.\n"
844	>	"\tSorry, the ability to specify total"
845	>	" nMols and then give molfractions in the components\n"
846	>	"\tis not currently supported."
847	>	" Please give nMol in the components.\n");
848	>	painCave.isFatal = 1;
849	>	simError();
850	>	}
851
852	<	#ifdef IS_MPI
853	<	if( mpiSim->getMyMolStart() <= molIndex &&
854	<	molIndex <= mpiSim->getMyMolEnd() ){
855	<	#endif // is_mpi
852	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
853	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
854	>	sprintf(painCave.errMsg,
855	>	"Sample time is not divisible by dt.\n"
856	>	"\tThis will result in samples that are not uniformly\n"
857	>	"\tdistributed in time.  If this is a problem, change\n"
858	>	"\tyour sampleTime variable.\n");
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862
863	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
863	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
864	>	sprintf(painCave.errMsg,
865	>	"Status time is not divisible by dt.\n"
866	>	"\tThis will result in status reports that are not uniformly\n"
867	>	"\tdistributed in time.  If this is a problem, change \n"
868	>	"\tyour statusTime variable.\n");
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	}
872
873	<	current_torsion = comp_stamps[i]->getTorsion( k );
874	<	the_torsions[index].a = current_torsion->getA() + offset;
875	<	the_torsions[index].b = current_torsion->getB() + offset;
876	<	the_torsions[index].c = current_torsion->getC() + offset;
877	<	the_torsions[index].d = current_torsion->getD() + offset;
873	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
874	>	sprintf(painCave.errMsg,
875	>	"Thermal time is not divisible by dt.\n"
876	>	"\tThis will result in thermalizations that are not uniformly\n"
877	>	"\tdistributed in time.  If this is a problem, change \n"
878	>	"\tyour thermalTime variable.\n");
879	>	painCave.isFatal = 0;
880	>	simError();
881	>	}
882
883	<	exI = the_torsions[index].a;
884	<	exJ = the_torsions[index].d;
883	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
884	>	sprintf(painCave.errMsg,
885	>	"Reset time is not divisible by dt.\n"
886	>	"\tThis will result in integrator resets that are not uniformly\n"
887	>	"\tdistributed in time.  If this is a problem, change\n"
888	>	"\tyour resetTime variable.\n");
889	>	painCave.isFatal = 0;
890	>	simError();
891	>	}
892
893	<
938	<	// exclude_I must always be the smaller of the pair
939	<	if( exI > exJ ){
940	<	tempEx = exI;
941	<	exI = exJ;
942	<	exJ = tempEx;
943	<	}
893	>	// set the status, sample, and thermal kick times
894
895	+	for (i = 0; i < nInfo; i++){
896	+	if (globals->haveSampleTime()){
897	+	info[i].sampleTime = globals->getSampleTime();
898	+	info[i].statusTime = info[i].sampleTime;
899	+	}
900	+	else{
901	+	info[i].sampleTime = globals->getRunTime();
902	+	info[i].statusTime = info[i].sampleTime;
903	+	}
904
905	<	#ifdef IS_MPI
906	<
907	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
905	>	if (globals->haveStatusTime()){
906	>	info[i].statusTime = globals->getStatusTime();
907	>	}
908
909	<	// increment the index and repeat;
910	<	index++;
911	<	}
912	<	offset += comp_stamps[i]->getNAtoms();
909	>	if (globals->haveThermalTime()){
910	>	info[i].thermalTime = globals->getThermalTime();
911	>	} else {
912	>	info[i].thermalTime = globals->getRunTime();
913	>	}
914
915	<	#ifdef IS_MPI
916	<	}
917	<	#endif //is_mpi
918	<
970	<	molIndex++;
915	>	info[i].resetIntegrator = 0;
916	>	if( globals->haveResetTime() ){
917	>	info[i].resetTime = globals->getResetTime();
918	>	info[i].resetIntegrator = 1;
919		}
972	–	}
920
921	<	the_ff->initializeTorsions( the_torsions );
922	<	}
921	>	// check for the temperature set flag
922	>
923	>	if (globals->haveTempSet())
924	>	info[i].setTemp = globals->getTempSet();
925
926	<	void SimSetup::initFromBass( void ){
926	>	// check for the extended State init
927
928	<	int i, j, k;
929	<	int n_cells;
930	<	double cellx, celly, cellz;
931	<	double temp1, temp2, temp3;
932	<	int n_per_extra;
933	<	int n_extra;
934	<	int have_extra, done;
928	>	info[i].useInitXSstate = globals->getUseInitXSstate();
929	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
930	>
931	>	}
932	>
933	>	//setup seed for random number generator
934	>	int seedValue;
935
936	<	temp1 = (double)tot_nmol / 4.0;
937	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
989	<	temp3 = ceil( temp2 );
936	>	if (globals->haveSeed()){
937	>	seedValue = globals->getSeed();
938
939	<	have_extra =0;
940	<	if( temp2 < temp3 ){ // we have a non-complete lattice
941	<	have_extra =1;
942	<
943	<	n_cells = (int)temp3 - 1;
996	<	cellx = simnfo->box_x / temp3;
997	<	celly = simnfo->box_y / temp3;
998	<	cellz = simnfo->box_z / temp3;
999	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1000	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1001	<	n_per_extra = (int)ceil( temp1 );
1002	<
1003	<	if( n_per_extra > 4){
1004	<	sprintf( painCave.errMsg,
1005	<	"SimSetup error. There has been an error in constructing"
1006	<	" the non-complete lattice.\n" );
1007	<	painCave.isFatal = 1;
939	>	if(seedValue / 1E9 == 0){
940	>	sprintf(painCave.errMsg,
941	>	"Seed for sprng library should contain at least 9 digits\n"
942	>	"OOPSE will generate a seed for user\n");
943	>	painCave.isFatal = 0;
944		simError();
945	+
946	+	//using seed generated by system instead of invalid seed set by user
947	+	#ifndef IS_MPI
948	+	seedValue = make_sprng_seed();
949	+	#else
950	+	if (worldRank == 0){
951	+	seedValue = make_sprng_seed();
952	+	}
953	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
954	+	#endif
955		}
956	<	}
956	>	}//end of if branch of globals->haveSeed()
957		else{
958	<	n_cells = (int)temp3;
959	<	cellx = simnfo->box_x / temp3;
960	<	celly = simnfo->box_y / temp3;
961	<	cellz = simnfo->box_z / temp3;
958	>
959	>	#ifndef IS_MPI
960	>	seedValue = make_sprng_seed();
961	>	#else
962	>	if (worldRank == 0){
963	>	seedValue = make_sprng_seed();
964	>	}
965	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
966	>	#endif
967	>	}//end of globals->haveSeed()
968	>
969	>	for (int i = 0; i < nInfo; i++){
970	>	info[i].setSeed(seedValue);
971		}
972	+
973	+	#ifdef IS_MPI
974	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
975	+	MPIcheckPoint();
976	+	#endif // is_mpi
977	+	}
978
1018	–	current_mol = 0;
1019	–	current_comp_mol = 0;
1020	–	current_comp = 0;
1021	–	current_atom_ndx = 0;
979
980	<	for( i=0; i < n_cells ; i++ ){
981	<	for( j=0; j < n_cells; j++ ){
982	<	for( k=0; k < n_cells; k++ ){
980	>	void SimSetup::finalInfoCheck(void){
981	>	int index;
982	>	int usesDipoles;
983	>	int usesCharges;
984	>	int i;
985
986	<	makeElement( i * cellx,
987	<	j * celly,
1029	<	k * cellz );
986	>	for (i = 0; i < nInfo; i++){
987	>	// check electrostatic parameters
988
989	<	makeElement( i * cellx + 0.5 * cellx,
990	<	j * celly + 0.5 * celly,
991	<	k * cellz );
992	<
993	<	makeElement( i * cellx,
1036	<	j * celly + 0.5 * celly,
1037	<	k * cellz + 0.5 * cellz );
1038	<
1039	<	makeElement( i * cellx + 0.5 * cellx,
1040	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
1042	<	}
989	>	index = 0;
990	>	usesDipoles = 0;
991	>	while ((index < info[i].n_atoms) && !usesDipoles){
992	>	usesDipoles = (info[i].atoms[index])->hasDipole();
993	>	index++;
994		}
995	<	}
995	>	index = 0;
996	>	usesCharges = 0;
997	>	while ((index < info[i].n_atoms) && !usesCharges){
998	>	usesCharges= (info[i].atoms[index])->hasCharge();
999	>	index++;
1000	>	}
1001	>	#ifdef IS_MPI
1002	>	int myUse = usesDipoles;
1003	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1004	>	#endif //is_mpi
1005
1006	<	if( have_extra ){
1047	<	done = 0;
1006	>	double theRcut, theRsw;
1007
1008	<	int start_ndx;
1009	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1008	>	if (globals->haveRcut()) {
1009	>	theRcut = globals->getRcut();
1010
1011	<	if( i < n_cells ){
1011	>	if (globals->haveRsw())
1012	>	theRsw = globals->getRsw();
1013	>	else
1014	>	theRsw = theRcut;
1015	>
1016	>	info[i].setDefaultRcut(theRcut, theRsw);
1017
1018	<	if( j < n_cells ){
1019	<	start_ndx = n_cells;
1020	<	}
1021	<	else start_ndx = 0;
1059	<	}
1060	<	else start_ndx = 0;
1018	>	} else {
1019	>
1020	>	the_ff->calcRcut();
1021	>	theRcut = info[i].getRcut();
1022
1023	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1023	>	if (globals->haveRsw())
1024	>	theRsw = globals->getRsw();
1025	>	else
1026	>	theRsw = theRcut;
1027	>
1028	>	info[i].setDefaultRcut(theRcut, theRsw);
1029	>	}
1030
1031	<	makeElement( i * cellx,
1032	<	j * celly,
1033	<	k * cellz );
1034	<	done = ( current_mol >= tot_nmol );
1031	>	if (globals->getUseRF()){
1032	>	info[i].useReactionField = 1;
1033	>
1034	>	if (!globals->haveRcut()){
1035	>	sprintf(painCave.errMsg,
1036	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1037	>	"\tOOPSE will use a default value of 15.0 angstroms"
1038	>	"\tfor the cutoffRadius.\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	theRcut = 15.0;
1042	>	}
1043	>	else{
1044	>	theRcut = globals->getRcut();
1045	>	}
1046
1047	<	if( !done && n_per_extra > 1 ){
1048	<	makeElement( i * cellx + 0.5 * cellx,
1049	<	j * celly + 0.5 * celly,
1050	<	k * cellz );
1051	<	done = ( current_mol >= tot_nmol );
1052	<	}
1047	>	if (!globals->haveRsw()){
1048	>	sprintf(painCave.errMsg,
1049	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1050	>	"\tOOPSE will use a default value of\n"
1051	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1052	>	painCave.isFatal = 0;
1053	>	simError();
1054	>	theRsw = 0.95 * theRcut;
1055	>	}
1056	>	else{
1057	>	theRsw = globals->getRsw();
1058	>	}
1059
1060	<	if( !done && n_per_extra > 2){
1077	<	makeElement( i * cellx,
1078	<	j * celly + 0.5 * celly,
1079	<	k * cellz + 0.5 * cellz );
1080	<	done = ( current_mol >= tot_nmol );
1081	<	}
1060	>	info[i].setDefaultRcut(theRcut, theRsw);
1061
1062	<	if( !done && n_per_extra > 3){
1063	<	makeElement( i * cellx + 0.5 * cellx,
1064	<	j * celly,
1065	<	k * cellz + 0.5 * cellz );
1066	<	done = ( current_mol >= tot_nmol );
1067	<	}
1068	<	}
1062	>	if (!globals->haveDielectric()){
1063	>	sprintf(painCave.errMsg,
1064	>	"SimSetup Error: No Dielectric constant was set.\n"
1065	>	"\tYou are trying to use Reaction Field without"
1066	>	"\tsetting a dielectric constant!\n");
1067	>	painCave.isFatal = 1;
1068	>	simError();
1069		}
1070	+	info[i].dielectric = globals->getDielectric();
1071		}
1072	<	}
1072	>	else{
1073	>	if (usesDipoles || usesCharges){
1074
1075	<
1076	<	for( i=0; i<simnfo->n_atoms; i++ ){
1077	<	simnfo->atoms[i]->set_vx( 0.0 );
1078	<	simnfo->atoms[i]->set_vy( 0.0 );
1079	<	simnfo->atoms[i]->set_vz( 0.0 );
1075	>	if (!globals->haveRcut()){
1076	>	sprintf(painCave.errMsg,
1077	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1078	>	"\tOOPSE will use a default value of 15.0 angstroms"
1079	>	"\tfor the cutoffRadius.\n");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	theRcut = 15.0;
1083	>	}
1084	>	else{
1085	>	theRcut = globals->getRcut();
1086	>	}
1087	>
1088	>	if (!globals->haveRsw()){
1089	>	sprintf(painCave.errMsg,
1090	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1091	>	"\tOOPSE will use a default value of\n"
1092	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1093	>	painCave.isFatal = 0;
1094	>	simError();
1095	>	theRsw = 0.95 * theRcut;
1096	>	}
1097	>	else{
1098	>	theRsw = globals->getRsw();
1099	>	}
1100	>
1101	>	info[i].setDefaultRcut(theRcut, theRsw);
1102	>
1103	>	}
1104	>	}
1105		}
1106	+	#ifdef IS_MPI
1107	+	strcpy(checkPointMsg, "post processing checks out");
1108	+	MPIcheckPoint();
1109	+	#endif // is_mpi
1110	+
1111	+	// clean up the forcefield
1112	+	the_ff->cleanMe();
1113		}
1114	+
1115	+	void SimSetup::initSystemCoords(void){
1116	+	int i;
1117
1118	<	void SimSetup::makeElement( double x, double y, double z ){
1118	>	char* inName;
1119
1120	<	int k;
1105	<	AtomStamp* current_atom;
1106	<	DirectionalAtom* dAtom;
1107	<	double rotMat[3][3];
1120	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1121
1122	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1122	>	for (i = 0; i < info[0].n_atoms; i++)
1123	>	info[0].atoms[i]->setCoords();
1124
1125	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1126	<	if( !current_atom->havePosition() ){
1127	<	sprintf( painCave.errMsg,
1128	<	"SimSetup:initFromBass error.\n"
1129	<	"\tComponent %s, atom %s does not have a position specified.\n"
1130	<	"\tThe initialization routine is unable to give a start"
1131	<	" position.\n",
1132	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
1120	<	painCave.isFatal = 1;
1121	<	simError();
1125	>	if (globals->haveInitialConfig()){
1126	>	InitializeFromFile* fileInit;
1127	>	#ifdef IS_MPI // is_mpi
1128	>	if (worldRank == 0){
1129	>	#endif //is_mpi
1130	>	inName = globals->getInitialConfig();
1131	>	fileInit = new InitializeFromFile(inName);
1132	>	#ifdef IS_MPI
1133		}
1134	+	else
1135	+	fileInit = new InitializeFromFile(NULL);
1136	+	#endif
1137	+	fileInit->readInit(info); // default velocities on
1138
1139	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1140	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1141	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1139	>	delete fileInit;
1140	>	}
1141	>	else{
1142	>
1143	>	// no init from bass
1144	>
1145	>	sprintf(painCave.errMsg,
1146	>	"Cannot intialize a simulation without an initial configuration file.\n");
1147	>	painCave.isFatal = 1;;
1148	>	simError();
1149	>
1150	>	}
1151
1152	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1152	>	#ifdef IS_MPI
1153	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1154	>	MPIcheckPoint();
1155	>	#endif // is_mpi
1156	>	}
1157
1130	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1158
1159	<	rotMat[0][0] = 1.0;
1160	<	rotMat[0][1] = 0.0;
1134	<	rotMat[0][2] = 0.0;
1159	>	void SimSetup::makeOutNames(void){
1160	>	int k;
1161
1136	–	rotMat[1][0] = 0.0;
1137	–	rotMat[1][1] = 1.0;
1138	–	rotMat[1][2] = 0.0;
1162
1163	<	rotMat[2][0] = 0.0;
1164	<	rotMat[2][1] = 0.0;
1165	<	rotMat[2][2] = 1.0;
1163	>	for (k = 0; k < nInfo; k++){
1164	>	#ifdef IS_MPI
1165	>	if (worldRank == 0){
1166	>	#endif // is_mpi
1167
1168	<	dAtom->setA( rotMat );
1168	>	if (globals->haveFinalConfig()){
1169	>	strcpy(info[k].finalName, globals->getFinalConfig());
1170	>	}
1171	>	else{
1172	>	strcpy(info[k].finalName, inFileName);
1173	>	char* endTest;
1174	>	int nameLength = strlen(info[k].finalName);
1175	>	endTest = &(info[k].finalName[nameLength - 5]);
1176	>	if (!strcmp(endTest, ".bass")){
1177	>	strcpy(endTest, ".eor");
1178	>	}
1179	>	else if (!strcmp(endTest, ".BASS")){
1180	>	strcpy(endTest, ".eor");
1181	>	}
1182	>	else{
1183	>	endTest = &(info[k].finalName[nameLength - 4]);
1184	>	if (!strcmp(endTest, ".bss")){
1185	>	strcpy(endTest, ".eor");
1186	>	}
1187	>	else if (!strcmp(endTest, ".mdl")){
1188	>	strcpy(endTest, ".eor");
1189	>	}
1190	>	else{
1191	>	strcat(info[k].finalName, ".eor");
1192	>	}
1193	>	}
1194	>	}
1195	>
1196	>	// make the sample and status out names
1197	>
1198	>	strcpy(info[k].sampleName, inFileName);
1199	>	char* endTest;
1200	>	int nameLength = strlen(info[k].sampleName);
1201	>	endTest = &(info[k].sampleName[nameLength - 5]);
1202	>	if (!strcmp(endTest, ".bass")){
1203	>	strcpy(endTest, ".dump");
1204	>	}
1205	>	else if (!strcmp(endTest, ".BASS")){
1206	>	strcpy(endTest, ".dump");
1207	>	}
1208	>	else{
1209	>	endTest = &(info[k].sampleName[nameLength - 4]);
1210	>	if (!strcmp(endTest, ".bss")){
1211	>	strcpy(endTest, ".dump");
1212	>	}
1213	>	else if (!strcmp(endTest, ".mdl")){
1214	>	strcpy(endTest, ".dump");
1215	>	}
1216	>	else{
1217	>	strcat(info[k].sampleName, ".dump");
1218	>	}
1219	>	}
1220	>
1221	>	strcpy(info[k].statusName, inFileName);
1222	>	nameLength = strlen(info[k].statusName);
1223	>	endTest = &(info[k].statusName[nameLength - 5]);
1224	>	if (!strcmp(endTest, ".bass")){
1225	>	strcpy(endTest, ".stat");
1226	>	}
1227	>	else if (!strcmp(endTest, ".BASS")){
1228	>	strcpy(endTest, ".stat");
1229	>	}
1230	>	else{
1231	>	endTest = &(info[k].statusName[nameLength - 4]);
1232	>	if (!strcmp(endTest, ".bss")){
1233	>	strcpy(endTest, ".stat");
1234	>	}
1235	>	else if (!strcmp(endTest, ".mdl")){
1236	>	strcpy(endTest, ".stat");
1237	>	}
1238	>	else{
1239	>	strcat(info[k].statusName, ".stat");
1240	>	}
1241	>	}
1242	>
1243	>	#ifdef IS_MPI
1244	>
1245		}
1246	+	#endif // is_mpi
1247	+	}
1248	+	}
1249
1250	<	current_atom_ndx++;
1250	>
1251	>	void SimSetup::sysObjectsCreation(void){
1252	>	int i, k;
1253	>
1254	>	// create the forceField
1255	>
1256	>	createFF();
1257	>
1258	>	// extract componentList
1259	>
1260	>	compList();
1261	>
1262	>	// calc the number of atoms, bond, bends, and torsions
1263	>
1264	>	calcSysValues();
1265	>
1266	>	#ifdef IS_MPI
1267	>	// divide the molecules among the processors
1268	>
1269	>	mpiMolDivide();
1270	>	#endif //is_mpi
1271	>
1272	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1273	>
1274	>	makeSysArrays();
1275	>
1276	>	// make and initialize the molecules (all but atomic coordinates)
1277	>
1278	>	makeMolecules();
1279	>
1280	>	for (k = 0; k < nInfo; k++){
1281	>	info[k].identArray = new int[info[k].n_atoms];
1282	>	for (i = 0; i < info[k].n_atoms; i++){
1283	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1284	>	}
1285		}
1286	+	}
1287
1150	–	current_mol++;
1151	–	current_comp_mol++;
1288
1289	<	if( current_comp_mol >= components_nmol[current_comp] ){
1289	>	void SimSetup::createFF(void){
1290	>	switch (ffCase){
1291	>	case FF_DUFF:
1292	>	the_ff = new DUFF();
1293	>	break;
1294
1295	<	current_comp_mol = 0;
1296	<	current_comp++;
1295	>	case FF_LJ:
1296	>	the_ff = new LJFF();
1297	>	break;
1298	>
1299	>	case FF_EAM:
1300	>	the_ff = new EAM_FF();
1301	>	break;
1302	>
1303	>	case FF_H2O:
1304	>	the_ff = new WATER();
1305	>	break;
1306	>
1307	>	default:
1308	>	sprintf(painCave.errMsg,
1309	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1310	>	painCave.isFatal = 1;
1311	>	simError();
1312	>	}
1313	>
1314	>	#ifdef IS_MPI
1315	>	strcpy(checkPointMsg, "ForceField creation successful");
1316	>	MPIcheckPoint();
1317	>	#endif // is_mpi
1318	>	}
1319	>
1320	>
1321	>	void SimSetup::compList(void){
1322	>	int i;
1323	>	char* id;
1324	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1325	>	LinkedMolStamp* currentStamp = NULL;
1326	>	comp_stamps = new MoleculeStamp * [n_components];
1327	>	bool haveCutoffGroups;
1328	>
1329	>	haveCutoffGroups = false;
1330	>
1331	>	// make an array of molecule stamps that match the components used.
1332	>	// also extract the used stamps out into a separate linked list
1333	>
1334	>	for (i = 0; i < nInfo; i++){
1335	>	info[i].nComponents = n_components;
1336	>	info[i].componentsNmol = components_nmol;
1337	>	info[i].compStamps = comp_stamps;
1338	>	info[i].headStamp = headStamp;
1339	>	}
1340	>
1341	>
1342	>	for (i = 0; i < n_components; i++){
1343	>	id = the_components[i]->getType();
1344	>	comp_stamps[i] = NULL;
1345	>
1346	>	// check to make sure the component isn't already in the list
1347	>
1348	>	comp_stamps[i] = headStamp->match(id);
1349	>	if (comp_stamps[i] == NULL){
1350	>	// extract the component from the list;
1351	>
1352	>	currentStamp = stamps->extractMolStamp(id);
1353	>	if (currentStamp == NULL){
1354	>	sprintf(painCave.errMsg,
1355	>	"SimSetup error: Component \"%s\" was not found in the "
1356	>	"list of declared molecules\n",
1357	>	id);
1358	>	painCave.isFatal = 1;
1359	>	simError();
1360	>	}
1361	>
1362	>	headStamp->add(currentStamp);
1363	>	comp_stamps[i] = headStamp->match(id);
1364	>	}
1365	>
1366	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1367	>	haveCutoffGroups = true;
1368	>	}
1369	>
1370	>	for (i = 0; i < nInfo; i++)
1371	>	info[i].haveCutoffGroups = haveCutoffGroups;
1372	>
1373	>	#ifdef IS_MPI
1374	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1375	>	MPIcheckPoint();
1376	>	#endif // is_mpi
1377	>	}
1378	>
1379	>	void SimSetup::calcSysValues(void){
1380	>	int i;
1381	>
1382	>	int* molMembershipArray;
1383	>
1384	>	tot_atoms = 0;
1385	>	tot_bonds = 0;
1386	>	tot_bends = 0;
1387	>	tot_torsions = 0;
1388	>	tot_rigid = 0;
1389	>	for (i = 0; i < n_components; i++){
1390	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1391	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1392	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1393	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1394	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1395	>	}
1396	>
1397	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1398	>	molMembershipArray = new int[tot_atoms];
1399	>
1400	>	for (i = 0; i < nInfo; i++){
1401	>	info[i].n_atoms = tot_atoms;
1402	>	info[i].n_bonds = tot_bonds;
1403	>	info[i].n_bends = tot_bends;
1404	>	info[i].n_torsions = tot_torsions;
1405	>	info[i].n_SRI = tot_SRI;
1406	>	info[i].n_mol = tot_nmol;
1407	>
1408	>	info[i].molMembershipArray = molMembershipArray;
1409	>	}
1410	>	}
1411	>
1412	>	#ifdef IS_MPI
1413	>
1414	>	void SimSetup::mpiMolDivide(void){
1415	>	int i, j, k;
1416	>	int localMol, allMol;
1417	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1418	>	int local_rigid;
1419	>	vector<int> globalMolIndex;
1420	>
1421	>	mpiSim = new mpiSimulation(info);
1422	>
1423	>	mpiSim->divideLabor();
1424	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1425	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1426	>
1427	>	// set up the local variables
1428	>
1429	>	mol2proc = mpiSim->getMolToProcMap();
1430	>	molCompType = mpiSim->getMolComponentType();
1431	>
1432	>	allMol = 0;
1433	>	localMol = 0;
1434	>	local_atoms = 0;
1435	>	local_bonds = 0;
1436	>	local_bends = 0;
1437	>	local_torsions = 0;
1438	>	local_rigid = 0;
1439	>	globalAtomCounter = 0;
1440	>
1441	>	for (i = 0; i < n_components; i++){
1442	>	for (j = 0; j < components_nmol[i]; j++){
1443	>	if (mol2proc[allMol] == worldRank){
1444	>	local_atoms += comp_stamps[i]->getNAtoms();
1445	>	local_bonds += comp_stamps[i]->getNBonds();
1446	>	local_bends += comp_stamps[i]->getNBends();
1447	>	local_torsions += comp_stamps[i]->getNTorsions();
1448	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1449	>	localMol++;
1450	>	}
1451	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1452	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1453	>	globalAtomCounter++;
1454	>	}
1455	>
1456	>	allMol++;
1457	>	}
1458	>	}
1459	>	local_SRI = local_bonds + local_bends + local_torsions;
1460	>
1461	>	info[0].n_atoms = mpiSim->getMyNlocal();
1462	>
1463	>
1464	>	if (local_atoms != info[0].n_atoms){
1465	>	sprintf(painCave.errMsg,
1466	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1467	>	"\tlocalAtom (%d) are not equal.\n",
1468	>	info[0].n_atoms, local_atoms);
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472	>
1473	>	info[0].n_bonds = local_bonds;
1474	>	info[0].n_bends = local_bends;
1475	>	info[0].n_torsions = local_torsions;
1476	>	info[0].n_SRI = local_SRI;
1477	>	info[0].n_mol = localMol;
1478	>
1479	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1480	>	MPIcheckPoint();
1481	>	}
1482	>
1483	>	#endif // is_mpi
1484	>
1485	>
1486	>	void SimSetup::makeSysArrays(void){
1487	>
1488	>	#ifndef IS_MPI
1489	>	int k, j;
1490	>	#endif // is_mpi
1491	>	int i, l;
1492	>
1493	>	Atom** the_atoms;
1494	>	Molecule* the_molecules;
1495	>
1496	>	for (l = 0; l < nInfo; l++){
1497	>	// create the atom and short range interaction arrays
1498	>
1499	>	the_atoms = new Atom * [info[l].n_atoms];
1500	>	the_molecules = new Molecule[info[l].n_mol];
1501	>	int molIndex;
1502	>
1503	>	// initialize the molecule's stampID's
1504	>
1505	>	#ifdef IS_MPI
1506	>
1507	>
1508	>	molIndex = 0;
1509	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1510	>	if (mol2proc[i] == worldRank){
1511	>	the_molecules[molIndex].setStampID(molCompType[i]);
1512	>	the_molecules[molIndex].setMyIndex(molIndex);
1513	>	the_molecules[molIndex].setGlobalIndex(i);
1514	>	molIndex++;
1515	>	}
1516	>	}
1517	>
1518	>	#else // is_mpi
1519	>
1520	>	molIndex = 0;
1521	>	globalAtomCounter = 0;
1522	>	for (i = 0; i < n_components; i++){
1523	>	for (j = 0; j < components_nmol[i]; j++){
1524	>	the_molecules[molIndex].setStampID(i);
1525	>	the_molecules[molIndex].setMyIndex(molIndex);
1526	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1527	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1528	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1529	>	globalAtomCounter++;
1530	>	}
1531	>	molIndex++;
1532	>	}
1533	>	}
1534	>
1535	>
1536	>	#endif // is_mpi
1537	>
1538	>	info[l].globalExcludes = new int;
1539	>	info[l].globalExcludes[0] = 0;
1540	>
1541	>	// set the arrays into the SimInfo object
1542	>
1543	>	info[l].atoms = the_atoms;
1544	>	info[l].molecules = the_molecules;
1545	>	info[l].nGlobalExcludes = 0;
1546	>
1547	>	the_ff->setSimInfo(info);
1548	>	}
1549	>	}
1550	>
1551	>	void SimSetup::makeIntegrator(void){
1552	>	int k;
1553	>
1554	>	NVE<RealIntegrator>* myNVE = NULL;
1555	>	NVT<RealIntegrator>* myNVT = NULL;
1556	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1557	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1558	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1559	>
1560	>	for (k = 0; k < nInfo; k++){
1561	>	switch (ensembleCase){
1562	>	case NVE_ENS:
1563	>	if (globals->haveZconstraints()){
1564	>	setupZConstraint(info[k]);
1565	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1566	>	}
1567	>	else{
1568	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1569	>	}
1570	>
1571	>	info->the_integrator = myNVE;
1572	>	break;
1573	>
1574	>	case NVT_ENS:
1575	>	if (globals->haveZconstraints()){
1576	>	setupZConstraint(info[k]);
1577	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1578	>	}
1579	>	else
1580	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1581	>
1582	>	myNVT->setTargetTemp(globals->getTargetTemp());
1583	>
1584	>	if (globals->haveTauThermostat())
1585	>	myNVT->setTauThermostat(globals->getTauThermostat());
1586	>	else{
1587	>	sprintf(painCave.errMsg,
1588	>	"SimSetup error: If you use the NVT\n"
1589	>	"\tensemble, you must set tauThermostat.\n");
1590	>	painCave.isFatal = 1;
1591	>	simError();
1592	>	}
1593	>
1594	>	info->the_integrator = myNVT;
1595	>	break;
1596	>
1597	>	case NPTi_ENS:
1598	>	if (globals->haveZconstraints()){
1599	>	setupZConstraint(info[k]);
1600	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1601	>	}
1602	>	else
1603	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1604	>
1605	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1606	>
1607	>	if (globals->haveTargetPressure())
1608	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1609	>	else{
1610	>	sprintf(painCave.errMsg,
1611	>	"SimSetup error: If you use a constant pressure\n"
1612	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1613	>	painCave.isFatal = 1;
1614	>	simError();
1615	>	}
1616	>
1617	>	if (globals->haveTauThermostat())
1618	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1619	>	else{
1620	>	sprintf(painCave.errMsg,
1621	>	"SimSetup error: If you use an NPT\n"
1622	>	"\tensemble, you must set tauThermostat.\n");
1623	>	painCave.isFatal = 1;
1624	>	simError();
1625	>	}
1626	>
1627	>	if (globals->haveTauBarostat())
1628	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1629	>	else{
1630	>	sprintf(painCave.errMsg,
1631	>	"SimSetup error: If you use an NPT\n"
1632	>	"\tensemble, you must set tauBarostat.\n");
1633	>	painCave.isFatal = 1;
1634	>	simError();
1635	>	}
1636	>
1637	>	info->the_integrator = myNPTi;
1638	>	break;
1639	>
1640	>	case NPTf_ENS:
1641	>	if (globals->haveZconstraints()){
1642	>	setupZConstraint(info[k]);
1643	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1644	>	}
1645	>	else
1646	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1647	>
1648	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1649	>
1650	>	if (globals->haveTargetPressure())
1651	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1652	>	else{
1653	>	sprintf(painCave.errMsg,
1654	>	"SimSetup error: If you use a constant pressure\n"
1655	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1656	>	painCave.isFatal = 1;
1657	>	simError();
1658	>	}
1659	>
1660	>	if (globals->haveTauThermostat())
1661	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1662	>
1663	>	else{
1664	>	sprintf(painCave.errMsg,
1665	>	"SimSetup error: If you use an NPT\n"
1666	>	"\tensemble, you must set tauThermostat.\n");
1667	>	painCave.isFatal = 1;
1668	>	simError();
1669	>	}
1670	>
1671	>	if (globals->haveTauBarostat())
1672	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1673	>
1674	>	else{
1675	>	sprintf(painCave.errMsg,
1676	>	"SimSetup error: If you use an NPT\n"
1677	>	"\tensemble, you must set tauBarostat.\n");
1678	>	painCave.isFatal = 1;
1679	>	simError();
1680	>	}
1681	>
1682	>	info->the_integrator = myNPTf;
1683	>	break;
1684	>
1685	>	case NPTxyz_ENS:
1686	>	if (globals->haveZconstraints()){
1687	>	setupZConstraint(info[k]);
1688	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1689	>	}
1690	>	else
1691	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1692	>
1693	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1694	>
1695	>	if (globals->haveTargetPressure())
1696	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1697	>	else{
1698	>	sprintf(painCave.errMsg,
1699	>	"SimSetup error: If you use a constant pressure\n"
1700	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1701	>	painCave.isFatal = 1;
1702	>	simError();
1703	>	}
1704	>
1705	>	if (globals->haveTauThermostat())
1706	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1707	>	else{
1708	>	sprintf(painCave.errMsg,
1709	>	"SimSetup error: If you use an NPT\n"
1710	>	"\tensemble, you must set tauThermostat.\n");
1711	>	painCave.isFatal = 1;
1712	>	simError();
1713	>	}
1714	>
1715	>	if (globals->haveTauBarostat())
1716	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1717	>	else{
1718	>	sprintf(painCave.errMsg,
1719	>	"SimSetup error: If you use an NPT\n"
1720	>	"\tensemble, you must set tauBarostat.\n");
1721	>	painCave.isFatal = 1;
1722	>	simError();
1723	>	}
1724	>
1725	>	info->the_integrator = myNPTxyz;
1726	>	break;
1727	>
1728	>	default:
1729	>	sprintf(painCave.errMsg,
1730	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1731	>	painCave.isFatal = 1;
1732	>	simError();
1733	>	}
1734		}
1735		}
1736	+
1737	+	void SimSetup::initFortran(void){
1738	+	info[0].refreshSim();
1739	+
1740	+	if (!strcmp(info[0].mixingRule, "standard")){
1741	+	the_ff->initForceField(LB_MIXING_RULE);
1742	+	}
1743	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1744	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1745	+	}
1746	+	else{
1747	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1748	+	info[0].mixingRule);
1749	+	painCave.isFatal = 1;
1750	+	simError();
1751	+	}
1752	+
1753	+
1754	+	#ifdef IS_MPI
1755	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1756	+	MPIcheckPoint();
1757	+	#endif // is_mpi
1758	+	}
1759	+
1760	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1761	+	int nZConstraints;
1762	+	ZconStamp** zconStamp;
1763	+
1764	+	if (globals->haveZconstraintTime()){
1765	+	//add sample time of z-constraint  into SimInfo's property list
1766	+	DoubleData* zconsTimeProp = new DoubleData();
1767	+	zconsTimeProp->setID(ZCONSTIME_ID);
1768	+	zconsTimeProp->setData(globals->getZconsTime());
1769	+	theInfo.addProperty(zconsTimeProp);
1770	+	}
1771	+	else{
1772	+	sprintf(painCave.errMsg,
1773	+	"ZConstraint error: If you use a ZConstraint,\n"
1774	+	"\tyou must set zconsTime.\n");
1775	+	painCave.isFatal = 1;
1776	+	simError();
1777	+	}
1778	+
1779	+	//push zconsTol into siminfo, if user does not specify
1780	+	//value for zconsTol, a default value will be used
1781	+	DoubleData* zconsTol = new DoubleData();
1782	+	zconsTol->setID(ZCONSTOL_ID);
1783	+	if (globals->haveZconsTol()){
1784	+	zconsTol->setData(globals->getZconsTol());
1785	+	}
1786	+	else{
1787	+	double defaultZConsTol = 0.01;
1788	+	sprintf(painCave.errMsg,
1789	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1790	+	"\tOOPSE will use a default value of %f.\n"
1791	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1792	+	defaultZConsTol);
1793	+	painCave.isFatal = 0;
1794	+	simError();
1795	+
1796	+	zconsTol->setData(defaultZConsTol);
1797	+	}
1798	+	theInfo.addProperty(zconsTol);
1799	+
1800	+	//set Force Subtraction Policy
1801	+	StringData* zconsForcePolicy = new StringData();
1802	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1803	+
1804	+	if (globals->haveZconsForcePolicy()){
1805	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1806	+	}
1807	+	else{
1808	+	sprintf(painCave.errMsg,
1809	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1810	+	"\tOOPSE will use PolicyByMass.\n"
1811	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1812	+	painCave.isFatal = 0;
1813	+	simError();
1814	+	zconsForcePolicy->setData("BYMASS");
1815	+	}
1816	+
1817	+	theInfo.addProperty(zconsForcePolicy);
1818	+
1819	+	//set zcons gap
1820	+	DoubleData* zconsGap = new DoubleData();
1821	+	zconsGap->setID(ZCONSGAP_ID);
1822	+
1823	+	if (globals->haveZConsGap()){
1824	+	zconsGap->setData(globals->getZconsGap());
1825	+	theInfo.addProperty(zconsGap);
1826	+	}
1827	+
1828	+	//set zcons fixtime
1829	+	DoubleData* zconsFixtime = new DoubleData();
1830	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1831	+
1832	+	if (globals->haveZConsFixTime()){
1833	+	zconsFixtime->setData(globals->getZconsFixtime());
1834	+	theInfo.addProperty(zconsFixtime);
1835	+	}
1836	+
1837	+	//set zconsUsingSMD
1838	+	IntData* zconsUsingSMD = new IntData();
1839	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1840	+
1841	+	if (globals->haveZConsUsingSMD()){
1842	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1843	+	theInfo.addProperty(zconsUsingSMD);
1844	+	}
1845	+
1846	+	//Determine the name of ouput file and add it into SimInfo's property list
1847	+	//Be careful, do not use inFileName, since it is a pointer which
1848	+	//point to a string at master node, and slave nodes do not contain that string
1849	+
1850	+	string zconsOutput(theInfo.finalName);
1851	+
1852	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1853	+
1854	+	StringData* zconsFilename = new StringData();
1855	+	zconsFilename->setID(ZCONSFILENAME_ID);
1856	+	zconsFilename->setData(zconsOutput);
1857	+
1858	+	theInfo.addProperty(zconsFilename);
1859	+
1860	+	//setup index, pos and other parameters of z-constraint molecules
1861	+	nZConstraints = globals->getNzConstraints();
1862	+	theInfo.nZconstraints = nZConstraints;
1863	+
1864	+	zconStamp = globals->getZconStamp();
1865	+	ZConsParaItem tempParaItem;
1866	+
1867	+	ZConsParaData* zconsParaData = new ZConsParaData();
1868	+	zconsParaData->setID(ZCONSPARADATA_ID);
1869	+
1870	+	for (int i = 0; i < nZConstraints; i++){
1871	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1872	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1873	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1874	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1875	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1876	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1877	+	zconsParaData->addItem(tempParaItem);
1878	+	}
1879	+
1880	+	//check the uniqueness of index
1881	+	if(!zconsParaData->isIndexUnique()){
1882	+	sprintf(painCave.errMsg,
1883	+	"ZConstraint Error: molIndex is not unique!\n");
1884	+	painCave.isFatal = 1;
1885	+	simError();
1886	+	}
1887	+
1888	+	//sort the parameters by index of molecules
1889	+	zconsParaData->sortByIndex();
1890	+
1891	+	//push data into siminfo, therefore, we can retrieve later
1892	+	theInfo.addProperty(zconsParaData);
1893	+	}
1894	+
1895	+	void SimSetup::makeMinimizer(){
1896	+
1897	+	OOPSEMinimizer* myOOPSEMinimizer;
1898	+	MinimizerParameterSet* param;
1899	+	char minimizerName[100];
1900	+
1901	+	for (int i = 0; i < nInfo; i++){
1902	+
1903	+	//prepare parameter set for minimizer
1904	+	param = new MinimizerParameterSet();
1905	+	param->setDefaultParameter();
1906	+
1907	+	if (globals->haveMinimizer()){
1908	+	param->setFTol(globals->getMinFTol());
1909	+	}
1910	+
1911	+	if (globals->haveMinGTol()){
1912	+	param->setGTol(globals->getMinGTol());
1913	+	}
1914	+
1915	+	if (globals->haveMinMaxIter()){
1916	+	param->setMaxIteration(globals->getMinMaxIter());
1917	+	}
1918	+
1919	+	if (globals->haveMinWriteFrq()){
1920	+	param->setMaxIteration(globals->getMinMaxIter());
1921	+	}
1922	+
1923	+	if (globals->haveMinWriteFrq()){
1924	+	param->setWriteFrq(globals->getMinWriteFrq());
1925	+	}
1926	+
1927	+	if (globals->haveMinStepSize()){
1928	+	param->setStepSize(globals->getMinStepSize());
1929	+	}
1930	+
1931	+	if (globals->haveMinLSMaxIter()){
1932	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1933	+	}
1934	+
1935	+	if (globals->haveMinLSTol()){
1936	+	param->setLineSearchTol(globals->getMinLSTol());
1937	+	}
1938	+
1939	+	strcpy(minimizerName, globals->getMinimizer());
1940	+
1941	+	if (!strcasecmp(minimizerName, "CG")){
1942	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1943	+	}
1944	+	else if (!strcasecmp(minimizerName, "SD")){
1945	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1946	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1947	+	}
1948	+	else{
1949	+	sprintf(painCave.errMsg,
1950	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1951	+	painCave.isFatal = 0;
1952	+	simError();
1953	+
1954	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1955	+	}
1956	+	info[i].the_integrator = myOOPSEMinimizer;
1957	+
1958	+	//store the minimizer into simInfo
1959	+	info[i].the_minimizer = myOOPSEMinimizer;
1960	+	info[i].has_minimizer = true;
1961	+	}
1962	+
1963	+	}

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