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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 1212 by chrisfen, Tue Jun 1 17:15:43 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 "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
19		#include "mpiSimulation.hpp"
20		#endif
21
22	+	// some defines for ensemble and Forcefield  cases
23	+
24	+	#define NVE_ENS        0
25	+	#define NVT_ENS        1
26	+	#define NPTi_ENS       2
27	+	#define NPTf_ENS       3
28	+	#define NPTxyz_ENS     4
29	+
30	+
31	+	#define FF_DUFF  0
32	+	#define FF_LJ    1
33	+	#define FF_EAM   2
34	+	#define FF_H2O   3
35	+
36	+	using namespace std;
37	+
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 27 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
127	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// 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();
131	>	// creation of complex system objects
132
133	<	// 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 );
133	>	sysObjectsCreation();
134
135	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
135	>	// check on the post processing info
136
137	+	finalInfoCheck();
138
139	<	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	<	}
139	>	// initialize the system coordinates
140
141	<	#ifdef IS_MPI
142	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	+	if( !(globals->getUseInitTime()) )
145	+	info[0].currentTime = 0.0;
146	+	}
147	+
148	+	// make the output filenames
149	+
150	+	makeOutNames();
151
152	+	#ifdef IS_MPI
153	+	mpiSim->mpiRefresh();
154	+	#endif
155
156	<	// 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];
156	>	// initialize the Fortran
157
158	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
158	>	initFortran();
159
160	<	tot_nmol = 0;
161	<	for( i=0; i<n_components; i++ ){
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	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	<	}
167	>	}
168
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	–	}
169
170	<	#ifdef IS_MPI
171	<	strcpy( checkPointMsg, "Have the number of components" );
172	<	MPIcheckPoint();
173	<	#endif // is_mpi
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI;
175	>	int stampID, atomOffset, rbOffset;
176	>	molInit molInfo;
177	>	DirectionalAtom* dAtom;
178	>	RigidBody* myRB;
179	>	StuntDouble* mySD;
180	>	LinkedAssign* extras;
181	>	LinkedAssign* current_extra;
182	>	AtomStamp* currentAtom;
183	>	BondStamp* currentBond;
184	>	BendStamp* currentBend;
185	>	TorsionStamp* currentTorsion;
186	>	RigidBodyStamp* currentRigidBody;
187	>	CutoffGroupStamp* currentCutoffGroup;
188	>	CutoffGroup* myCutoffGroup;
189	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192	<	// make an array of molecule stamps that match the components used.
193	<	// also extract the used stamps out into a separate linked list
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	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++ ){
196	>	set<int> skipList;
197
198	<	id = the_components[i]->getType();
199	<	comp_stamps[i] = NULL;
200	<
181	<	// check to make sure the component isn't already in the list
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	<	comp_stamps[i] = headStamp->match( id );
203	<	if( comp_stamps[i] == NULL ){
204	<
205	<	// extract the component from the list;
206	<
207	<	currentStamp = the_stamps->extractMolStamp( id );
208	<	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	<	}
202	>	//ConstraintPair* consPair; //constraint pair
203	>	//ConstraintElement* consElement1;  //first element of constraint pair
204	>	//ConstraintElement* consElement2;  //second element of constraint pair
205	>	//int whichRigidBody;
206	>	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	>	//vector<pair<int, int> > jointAtoms;
208	>	//init the forceField paramters
209
210	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
210	>	the_ff->readParams();
211
212	+	// init the atoms
213
214	+	int nMembers, nNew, rb1, rb2;
215
216	<	// caclulate the number of atoms, bonds, bends and torsions
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
219	<	tot_atoms = 0;
220	<	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	<	}
219	>	atomOffset = 0;
220	>	groupOffset = 0;
221
222	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
222	>	for (i = 0; i < info[k].n_mol; i++){
223	>	stampID = info[k].molecules[i].getStampID();
224	>	molName = comp_stamps[stampID]->getID();
225
226	<	simnfo->n_atoms = tot_atoms;
227	<	simnfo->n_bonds = tot_bonds;
228	<	simnfo->n_bends = tot_bends;
229	<	simnfo->n_torsions = tot_torsions;
230	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
226	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
229	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231
232	<
233	<	#ifdef IS_MPI
232	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233	>
234	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
235
236	<	// divide the molecules among processors here.
237	<
238	<	mpiSim = new mpiSimulation( simnfo );
239	<
241	<
236	>	if (molInfo.nBonds > 0)
237	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	>	else
239	>	molInfo.myBonds = NULL;
240
241	<	globalIndex = mpiSim->divideLabor();
241	>	if (molInfo.nBends > 0)
242	>	molInfo.myBends = new Bend*[molInfo.nBends];
243	>	else
244	>	molInfo.myBends = NULL;
245
246	+	if (molInfo.nTorsions > 0)
247	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	+	else
249	+	molInfo.myTorsions = NULL;
250
251	<
252	<	// set up the local variables
253	<
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++ ){
251	>	theBonds = new bond_pair[molInfo.nBonds];
252	>	theBends = new bend_set[molInfo.nBends];
253	>	theTorsions = new torsion_set[molInfo.nTorsions];
254
255	<	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	<
255	>	// make the Atoms
256
257	<	simnfo->n_atoms = mpiSim->getMyNlocal();
258	<
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	<	}
257	>	for (j = 0; j < molInfo.nAtoms; j++){
258	>	currentAtom = comp_stamps[stampID]->getAtom(j);
259
260	<	simnfo->n_bonds = local_bonds;
261	<	simnfo->n_bends = local_bends;
262	<	simnfo->n_torsions = local_torsions;
263	<	simnfo->n_SRI = local_SRI;
264	<	simnfo->n_mol = localMol;
260	>	if (currentAtom->haveOrientation()){
261	>	dAtom = new DirectionalAtom((j + atomOffset),
262	>	info[k].getConfiguration());
263	>	info[k].n_oriented++;
264	>	molInfo.myAtoms[j] = dAtom;
265
266	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
267	<	MPIcheckPoint();
268	<
298	<
299	<	#endif // is_mpi
300	<
266	>	// Directional Atoms have standard unit vectors which are oriented
267	>	// in space using the three Euler angles.  We assume the standard
268	>	// unit vector was originally along the z axis below.
269
270	<	// create the atom and short range interaction arrays
270	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
271	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
272	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
273
274	<	Atom::createArrays(simnfo->n_atoms);
275	<	the_atoms = new Atom*[simnfo->n_atoms];
276	<	the_molecules = new Molecule[simnfo->n_mol];
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275	>
276	>	}
277	>	else{
278
279	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280
281	<	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;
281	>	}
282
283	<	simnfo->n_exclude = 1;
284	<	}
283	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
284	>	#ifdef IS_MPI
285
286	<	// set the arrays into the SimInfo object
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
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();
288		#endif // is_mpi
289	<
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() ){
289	>	}
290
291	<	double vol;
292	<	vol = (double)tot_nmol / the_globals->getDensity();
293	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
294	<	simnfo->box_y = simnfo->box_x;
295	<	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();
291	>	// make the bonds
292	>	for (j = 0; j < molInfo.nBonds; j++){
293	>	currentBond = comp_stamps[stampID]->getBond(j);
294	>	theBonds[j].a = currentBond->getA() + atomOffset;
295	>	theBonds[j].b = currentBond->getB() + atomOffset;
296
297	<	if( !the_globals->haveBoxY() ){
298	<	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();
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299
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	–
300		#ifdef IS_MPI
301	<	strcpy( checkPointMsg, "Box size set up" );
302	<	MPIcheckPoint();
303	<	#endif // is_mpi
301	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
302	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
303	>	#else
304	>	exI = tempI + 1;
305	>	exJ = tempJ + 1;
306	>	#endif
307
308	+	info[k].excludes->addPair(exI, exJ);
309	+	}
310
311	<	// initialize the arrays
311	>	//make the bends
312	>	for (j = 0; j < molInfo.nBends; j++){
313	>	currentBend = comp_stamps[stampID]->getBend(j);
314	>	theBends[j].a = currentBend->getA() + atomOffset;
315	>	theBends[j].b = currentBend->getB() + atomOffset;
316	>	theBends[j].c = currentBend->getC() + atomOffset;
317
318	<	the_ff->setSimInfo( simnfo );
318	>	if (currentBend->haveExtras()){
319	>	extras = currentBend->getExtras();
320	>	current_extra = extras;
321
322	<	makeAtoms();
323	<	simnfo->identArray = new int[simnfo->n_atoms];
324	<	for(i=0; i<simnfo->n_atoms; i++){
325	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
326	<	}
327	<
328	<	if( tot_bonds ){
417	<	makeBonds();
418	<	}
322	>	while (current_extra != NULL){
323	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
324	>	switch (current_extra->getType()){
325	>	case 0:
326	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
327	>	theBends[j].isGhost = 1;
328	>	break;
329
330	<	if( tot_bends ){
331	<	makeBends();
332	<	}
330	>	case 1:
331	>	theBends[j].ghost = (int) current_extra->getDouble() +
332	>	atomOffset;
333	>	theBends[j].isGhost = 1;
334	>	break;
335
336	<	if( tot_torsions ){
337	<	makeTorsions();
338	<	}
336	>	default:
337	>	sprintf(painCave.errMsg,
338	>	"SimSetup Error: ghostVectorSource was neither a "
339	>	"double nor an int.\n"
340	>	"-->Bend[%d] in %s\n",
341	>	j, comp_stamps[stampID]->getID());
342	>	painCave.isFatal = 1;
343	>	simError();
344	>	}
345	>	}
346	>	else{
347	>	sprintf(painCave.errMsg,
348	>	"SimSetup Error: unhandled bend assignment:\n"
349	>	"    -->%s in Bend[%d] in %s\n",
350	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354
355	+	current_extra = current_extra->getNext();
356	+	}
357	+	}
358
359	+	if (theBends[j].isGhost) {
360	+
361	+	tempI = theBends[j].a;
362	+	tempJ = theBends[j].b;
363	+
364	+	#ifdef IS_MPI
365	+	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	+	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	+	#else
368	+	exI = tempI + 1;
369	+	exJ = tempJ + 1;
370	+	#endif
371	+	info[k].excludes->addPair(exI, exJ);
372
373	+	} else {
374
375	<
376	<
377	<	if( the_globals->haveInitialConfig() ){
378	<
435	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>	tempK = theBends[j].c;
378	>
379		#ifdef IS_MPI
380	<	}else fileInit = new InitializeFromFile( NULL );
380	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
381	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
382	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
383	>	#else
384	>	exI = tempI + 1;
385	>	exJ = tempJ + 1;
386	>	exK = tempK + 1;
387		#endif
388	<	fileInit->read_xyz( simnfo ); // default velocities on
388	>
389	>	info[k].excludes->addPair(exI, exK);
390	>	info[k].excludes->addPair(exI, exJ);
391	>	info[k].excludes->addPair(exJ, exK);
392	>	}
393	>	}
394
395	<	delete fileInit;
396	<	}
397	<	else{
395	>	for (j = 0; j < molInfo.nTorsions; j++){
396	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
397	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
398	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
399	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
400	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
401
402	<	#ifdef IS_MPI
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406
407	<	// no init from bass
408	<
409	<	sprintf( painCave.errMsg,
410	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
411	<	painCave.isFatal;
456	<	simError();
457	<
407	>	#ifdef IS_MPI
408	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
409	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
410	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
411	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
412		#else
413	<
414	<	initFromBass();
415	<
416	<
413	>	exI = tempI + 1;
414	>	exJ = tempJ + 1;
415	>	exK = tempK + 1;
416	>	exL = tempL + 1;
417		#endif
464	–	}
418
419	<	#ifdef IS_MPI
420	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
421	<	MPIcheckPoint();
422	<	#endif // is_mpi
423	<
424	<
472	<
473	<
474	<
475	<
476	<
477	<	#ifdef IS_MPI
478	<	if( worldRank == 0 ){
479	<	#endif // is_mpi
480	<
481	<	if( the_globals->haveFinalConfig() ){
482	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
483	<	}
484	<	else{
485	<	strcpy( simnfo->finalName, inFileName );
486	<	char* endTest;
487	<	int nameLength = strlen( simnfo->finalName );
488	<	endTest = &(simnfo->finalName[nameLength - 5]);
489	<	if( !strcmp( endTest, ".bass" ) ){
490	<	strcpy( endTest, ".eor" );
419	>	info[k].excludes->addPair(exI, exJ);
420	>	info[k].excludes->addPair(exI, exK);
421	>	info[k].excludes->addPair(exI, exL);
422	>	info[k].excludes->addPair(exJ, exK);
423	>	info[k].excludes->addPair(exJ, exL);
424	>	info[k].excludes->addPair(exK, exL);
425		}
492	–	else if( !strcmp( endTest, ".BASS" ) ){
493	–	strcpy( endTest, ".eor" );
494	–	}
495	–	else{
496	–	endTest = &(simnfo->finalName[nameLength - 4]);
497	–	if( !strcmp( endTest, ".bss" ) ){
498	–	strcpy( endTest, ".eor" );
499	–	}
500	–	else if( !strcmp( endTest, ".mdl" ) ){
501	–	strcpy( endTest, ".eor" );
502	–	}
503	–	else{
504	–	strcat( simnfo->finalName, ".eor" );
505	–	}
506	–	}
507	–	}
508	–
509	–	// make the sample and status out names
510	–
511	–	strcpy( simnfo->sampleName, inFileName );
512	–	char* endTest;
513	–	int nameLength = strlen( simnfo->sampleName );
514	–	endTest = &(simnfo->sampleName[nameLength - 5]);
515	–	if( !strcmp( endTest, ".bass" ) ){
516	–	strcpy( endTest, ".dump" );
517	–	}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
521	–	else{
522	–	endTest = &(simnfo->sampleName[nameLength - 4]);
523	–	if( !strcmp( endTest, ".bss" ) ){
524	–	strcpy( endTest, ".dump" );
525	–	}
526	–	else if( !strcmp( endTest, ".mdl" ) ){
527	–	strcpy( endTest, ".dump" );
528	–	}
529	–	else{
530	–	strcat( simnfo->sampleName, ".dump" );
531	–	}
532	–	}
533	–
534	–	strcpy( simnfo->statusName, inFileName );
535	–	nameLength = strlen( simnfo->statusName );
536	–	endTest = &(simnfo->statusName[nameLength - 5]);
537	–	if( !strcmp( endTest, ".bass" ) ){
538	–	strcpy( endTest, ".stat" );
539	–	}
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" );
550	–	}
551	–	else{
552	–	strcat( simnfo->statusName, ".stat" );
553	–	}
554	–	}
555	–
556	–	#ifdef IS_MPI
557	–	}
558	–	#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	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	–	}
426
427	<	if( the_globals->haveStatusTime() ){
428	<	simnfo->statusTime = the_globals->getStatusTime();
429	<	}
427	>
428	>	molInfo.myRigidBodies.clear();
429	>
430	>	for (j = 0; j < molInfo.nRigidBodies; j++){
431
432	<	if( the_globals->haveThermalTime() ){
433	<	simnfo->thermalTime = the_globals->getThermalTime();
579	<	}
432	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
433	>	nMembers = currentRigidBody->getNMembers();
434
435	<	// check for the temperature set flag
435	>	// Create the Rigid Body:
436
437	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
437	>	myRB = new RigidBody();
438
439	+	sprintf(rbName,"%s_RB_%d", molName, j);
440	+	myRB->setType(rbName);
441	+
442	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
443
444	<	//   // make the longe range forces and the integrator
444	>	// molI is atom numbering inside this molecule
445	>	molI = currentRigidBody->getMember(rb1);
446
447	<	//   new AllLong( simnfo );
448	<
590	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
592	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
594	<
595	<
596	<
597	<	// initialize the Fortran
598	<
599	<	simnfo->refreshSim();
600	<
601	<	if( !strcmp( simnfo->mixingRule, "standard") ){
602	<	the_ff->initForceField( LB_MIXING_RULE );
603	<	}
604	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
605	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
606	<	}
607	<	else{
608	<	sprintf( painCave.errMsg,
609	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
610	<	simnfo->mixingRule );
611	<	painCave.isFatal = 1;
612	<	simError();
613	<	}
447	>	// tempI is atom numbering on local processor
448	>	tempI = molI + atomOffset;
449
450	+	// currentAtom is the AtomStamp (which we need for
451	+	// rigid body reference positions)
452	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
453
454	+	// When we add to the rigid body, add the atom itself and
455	+	// the stamp info:
456	+
457	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
458	+
459	+	// Add this atom to the Skip List for the integrators
460		#ifdef IS_MPI
461	<	strcpy( checkPointMsg,
462	<	"Successfully intialized the mixingRule for Fortran." );
463	<	MPIcheckPoint();
464	<	#endif // is_mpi
465	<	}
461	>	slI = info[k].atoms[tempI]->getGlobalIndex();
462	>	#else
463	>	slI = tempI;
464	>	#endif
465	>	skipList.insert(slI);
466	>
467	>	}
468	>
469	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
470	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
471	>
472	>	tempI = currentRigidBody->getMember(rb1);
473	>	tempJ = currentRigidBody->getMember(rb2);
474	>
475	>	// Some explanation is required here.
476	>	// Fortran indexing starts at 1, while c indexing starts at 0
477	>	// Also, in parallel computations, the GlobalIndex is
478	>	// used for the exclude list:
479	>
480	>	#ifdef IS_MPI
481	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483	>	#else
484	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486	>	#endif
487	>
488	>	info[k].excludes->addPair(exI, exJ);
489	>
490	>	}
491	>	}
492
493	<	void SimSetup::makeAtoms( void ){
493	>	molInfo.myRigidBodies.push_back(myRB);
494	>	info[k].rigidBodies.push_back(myRB);
495	>	}
496	>
497
498	<	int i, j, k, index;
626	<	double ux, uy, uz, uSqr, u;
627	<	AtomStamp* current_atom;
498	>	//create cutoff group for molecule
499
500	<	DirectionalAtom* dAtom;
501	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
500	>	cutoffAtomSet.clear();
501	>	molInfo.myCutoffGroups.clear();
502	>
503	>	for (j = 0; j < nCutoffGroups; j++){
504
505	<	lMolIndex = 0;
506	<	molIndex = 0;
634	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
505	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	>	nMembers = currentCutoffGroup->getNMembers();
507
508	<	for( j=0; j<components_nmol[i]; j++ ){
508	>	myCutoffGroup = new CutoffGroup();
509	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	>
511	>	for (int cg = 0; cg < nMembers; cg++) {
512
513	+	// molI is atom numbering inside this molecule
514	+	molI = currentCutoffGroup->getMember(cg);
515	+
516	+	// tempI is atom numbering on local processor
517	+	tempI = molI + atomOffset;
518	+
519		#ifdef IS_MPI
520	<	if( mpiSim->getMyMolStart() <= molIndex &&
521	<	molIndex <= mpiSim->getMyMolEnd() ){
522	<	#endif // is_mpi
520	>	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	>	#else
522	>	globalID = info[k].atoms[tempI]->getIndex();
523	>	#endif
524
525	<	molStart = index;
645	<	nMemb = comp_stamps[i]->getNAtoms();
646	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647	<
648	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
525	>	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526
527	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528	+
529	+	cutoffAtomSet.insert(tempI);
530	+	}
531	+
532	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	+	groupOffset++;
534	+
535	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536	+
537	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
538	+
539	+	for(j = 0; j < molInfo.nAtoms; j++){
540	+
541	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	+	myCutoffGroup = new CutoffGroup();
543	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545		#ifdef IS_MPI
546	+	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	+	#else
548	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	+	#endif
550	+	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	+	groupOffset++;
553	+	}
554	+
555		}
556	<	#endif //is_mpi
556	>
557	>	// After this is all set up, scan through the atoms to
558	>	// see if they can be added to the integrableObjects:
559	>
560	>	molInfo.myIntegrableObjects.clear();
561
691	–	molIndex++;
692	–	}
693	–	}
562
563	+	for (j = 0; j < molInfo.nAtoms; j++){
564	+
565		#ifdef IS_MPI
566	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
567	<
568	<	delete[] globalIndex;
566	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	>	#else
568	>	slJ = j+atomOffset;
569	>	#endif
570
571	<	mpiSim->mpiRefresh();
701	<	#endif //IS_MPI
702	<
703	<	the_ff->initializeAtoms();
704	<	}
571	>	// if they aren't on the skip list, then they can be integrated
572
573	<	void SimSetup::makeBonds( void ){
573	>	if (skipList.find(slJ) == skipList.end()) {
574	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	>	info[k].integrableObjects.push_back(mySD);
576	>	molInfo.myIntegrableObjects.push_back(mySD);
577	>	}
578	>	}
579
580	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
580	>	// all rigid bodies are integrated:
581
582	<	the_bonds = new bond_pair[tot_bonds];
583	<	index = 0;
584	<	offset = 0;
585	<	molIndex = 0;
582	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	>	info[k].integrableObjects.push_back(mySD);
585	>	molInfo.myIntegrableObjects.push_back(mySD);
586	>	}
587
717	–	for( i=0; i<n_components; i++ ){
588
589	<	for( j=0; j<components_nmol[i]; j++ ){
589	>	/*
590
591	<	#ifdef IS_MPI
592	<	if( mpiSim->getMyMolStart() <= molIndex &&
593	<	molIndex <= mpiSim->getMyMolEnd() ){
594	<	#endif // is_mpi
595	<
596	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
597	<
598	<	current_bond = comp_stamps[i]->getBond( k );
599	<	the_bonds[index].a = current_bond->getA() + offset;
600	<	the_bonds[index].b = current_bond->getB() + offset;
591	>	//creat ConstraintPair.
592	>	molInfo.myConstraintPair.clear();
593	>
594	>	for (j = 0; j < molInfo.nBonds; j++){
595	>
596	>	//if both atoms are in the same rigid body, just skip it
597	>	currentBond = comp_stamps[stampID]->getBond(j);
598	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	>
600	>	tempI = currentBond->getA() + atomOffset;
601	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	>	else
604	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	>
606	>	tempJ =  currentBond->getB() + atomOffset;
607	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	>	else
610	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611
612	<	exI = the_bonds[index].a;
613	<	exJ = the_bonds[index].b;
612	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	>	molInfo.myConstraintPairs.push_back(consPair);
614	>	}
615	>	}
616	>
617	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	>
621	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622
623	<	// exclude_I must always be the smaller of the pair
624	<	if( exI > exJ ){
625	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
623	>	for(size_t m = 0; m < jointAtoms.size(); m++){
624	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626
627	<
628	<	#ifdef IS_MPI
627	>	consPair = new JointConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630
631	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
749	<
750	<	#else  // isn't MPI
751	<
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
631	>	}
632		}
764	–	#endif //is_mpi
633
634	<	molIndex++;
635	<	}
636	<	}
634	>	*/
635	>	// send the arrays off to the forceField for init.
636	>
637	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
638	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
639	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
640	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
641	>	theTorsions);
642
643	<	the_ff->initializeBonds( the_bonds );
771	<	}
643	>	info[k].molecules[i].initialize(molInfo);
644
773	–	void SimSetup::makeBends( void ){
645
646	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
647	<	bend_set* the_bends;
648	<	BendStamp* current_bend;
649	<	LinkedAssign* extras;
650	<	LinkedAssign* current_extra;
780	<
781	<
782	<	the_bends = new bend_set[tot_bends];
783	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
786	<	for( i=0; i<n_components; i++ ){
787	<
788	<	for( j=0; j<components_nmol[i]; j++ ){
789	<
790	<	#ifdef IS_MPI
791	<	if( mpiSim->getMyMolStart() <= molIndex &&
792	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
794	<
795	<	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	<	}
867	<
868	<
869	<	#ifdef IS_MPI
870	<
871	<	the_excludes[(index + tot_bonds)*2] =
872	<	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
892	<
893	<	molIndex++;
894	<	}
646	>	atomOffset += molInfo.nAtoms;
647	>	delete[] theBonds;
648	>	delete[] theBends;
649	>	delete[] theTorsions;
650	>	}
651		}
652
653		#ifdef IS_MPI
654	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
654	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
655		MPIcheckPoint();
656		#endif // is_mpi
902	–
657
904	–	the_ff->initializeBends( the_bends );
658		}
659
660	<	void SimSetup::makeTorsions( void ){
908	<
909	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910	<	torsion_set* the_torsions;
911	<	TorsionStamp* current_torsion;
912	<
913	<	the_torsions = new torsion_set[tot_torsions];
914	<	index = 0;
915	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
918	<
919	<	for( j=0; j<components_nmol[i]; j++ ){
920	<
921	<	#ifdef IS_MPI
922	<	if( mpiSim->getMyMolStart() <= molIndex &&
923	<	molIndex <= mpiSim->getMyMolEnd() ){
924	<	#endif // is_mpi
925	<
926	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
927	<
928	<	current_torsion = comp_stamps[i]->getTorsion( k );
929	<	the_torsions[index].a = current_torsion->getA() + offset;
930	<	the_torsions[index].b = current_torsion->getB() + offset;
931	<	the_torsions[index].c = current_torsion->getC() + offset;
932	<	the_torsions[index].d = current_torsion->getD() + offset;
933	<
934	<	exI = the_torsions[index].a;
935	<	exJ = the_torsions[index].d;
936	<
937	<
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	<	}
944	<
945	<
946	<	#ifdef IS_MPI
947	<
948	<	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	<
960	<
961	<	// increment the index and repeat;
962	<	index++;
963	<	}
964	<	offset += comp_stamps[i]->getNAtoms();
965	<
966	<	#ifdef IS_MPI
967	<	}
968	<	#endif //is_mpi
969	<
970	<	molIndex++;
971	<	}
972	<	}
973	<
974	<	the_ff->initializeTorsions( the_torsions );
975	<	}
976	<
977	<	void SimSetup::initFromBass( void ){
978	<
660	>	void SimSetup::initFromBass(void){
661		int i, j, k;
662		int n_cells;
663		double cellx, celly, cellz;
#	Line 984 | Line 666 | void SimSetup::initFromBass( void ){
666		int n_extra;
667		int have_extra, done;
668
669	<	temp1 = (double)tot_nmol / 4.0;
670	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
671	<	temp3 = ceil( temp2 );
669	>	double vel[3];
670	>	vel[0] = 0.0;
671	>	vel[1] = 0.0;
672	>	vel[2] = 0.0;
673
674	<	have_extra =0;
675	<	if( temp2 < temp3 ){ // we have a non-complete lattice
676	<	have_extra =1;
674	>	temp1 = (double) tot_nmol / 4.0;
675	>	temp2 = pow(temp1, (1.0 / 3.0));
676	>	temp3 = ceil(temp2);
677
678	<	n_cells = (int)temp3 - 1;
679	<	cellx = simnfo->box_x / temp3;
680	<	celly = simnfo->box_y / temp3;
681	<	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 );
678	>	have_extra = 0;
679	>	if (temp2 < temp3){
680	>	// we have a non-complete lattice
681	>	have_extra = 1;
682
683	<	if( n_per_extra > 4){
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error. There has been an error in constructing"
686	<	" the non-complete lattice.\n" );
683	>	n_cells = (int) temp3 - 1;
684	>	cellx = info[0].boxL[0] / temp3;
685	>	celly = info[0].boxL[1] / temp3;
686	>	cellz = info[0].boxL[2] / temp3;
687	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
688	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
689	>	n_per_extra = (int) ceil(temp1);
690	>
691	>	if (n_per_extra > 4){
692	>	sprintf(painCave.errMsg,
693	>	"SimSetup error. There has been an error in constructing"
694	>	" the non-complete lattice.\n");
695		painCave.isFatal = 1;
696		simError();
697		}
698		}
699		else{
700	<	n_cells = (int)temp3;
701	<	cellx = simnfo->box_x / temp3;
702	<	celly = simnfo->box_y / temp3;
703	<	cellz = simnfo->box_z / temp3;
700	>	n_cells = (int) temp3;
701	>	cellx = info[0].boxL[0] / temp3;
702	>	celly = info[0].boxL[1] / temp3;
703	>	cellz = info[0].boxL[2] / temp3;
704		}
705
706		current_mol = 0;
#	Line 1020 | Line 708 | void SimSetup::initFromBass( void ){
708		current_comp = 0;
709		current_atom_ndx = 0;
710
711	<	for( i=0; i < n_cells ; i++ ){
712	<	for( j=0; j < n_cells; j++ ){
713	<	for( k=0; k < n_cells; k++ ){
711	>	for (i = 0; i < n_cells ; i++){
712	>	for (j = 0; j < n_cells; j++){
713	>	for (k = 0; k < n_cells; k++){
714	>	makeElement(i * cellx, j * celly, k * cellz);
715
716	<	makeElement( i * cellx,
1028	<	j * celly,
1029	<	k * cellz );
716	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
717
718	<	makeElement( i * cellx + 0.5 * cellx,
1032	<	j * celly + 0.5 * celly,
1033	<	k * cellz );
718	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
719
720	<	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 );
720	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
721		}
722		}
723		}
724
725	<	if( have_extra ){
725	>	if (have_extra){
726		done = 0;
727
728		int start_ndx;
729	<	for( i=0; i < (n_cells+1) && !done; i++ ){
730	<	for( j=0; j < (n_cells+1) && !done; j++ ){
729	>	for (i = 0; i < (n_cells + 1) && !done; i++){
730	>	for (j = 0; j < (n_cells + 1) && !done; j++){
731	>	if (i < n_cells){
732	>	if (j < n_cells){
733	>	start_ndx = n_cells;
734	>	}
735	>	else
736	>	start_ndx = 0;
737	>	}
738	>	else
739	>	start_ndx = 0;
740
741	<	if( i < n_cells ){
741	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
742	>	makeElement(i * cellx, j * celly, k * cellz);
743	>	done = (current_mol >= tot_nmol);
744
745	<	if( j < n_cells ){
746	<	start_ndx = n_cells;
747	<	}
748	<	else start_ndx = 0;
749	<	}
1060	<	else start_ndx = 0;
745	>	if (!done && n_per_extra > 1){
746	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
747	>	k * cellz);
748	>	done = (current_mol >= tot_nmol);
749	>	}
750
751	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
751	>	if (!done && n_per_extra > 2){
752	>	makeElement(i * cellx, j * celly + 0.5 * celly,
753	>	k * cellz + 0.5 * cellz);
754	>	done = (current_mol >= tot_nmol);
755	>	}
756
757	<	makeElement( i * cellx,
758	<	j * celly,
759	<	k * cellz );
760	<	done = ( current_mol >= tot_nmol );
761	<
762	<	if( !done && n_per_extra > 1 ){
1070	<	makeElement( i * cellx + 0.5 * cellx,
1071	<	j * celly + 0.5 * celly,
1072	<	k * cellz );
1073	<	done = ( current_mol >= tot_nmol );
1074	<	}
1075	<
1076	<	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	<	}
1082	<
1083	<	if( !done && n_per_extra > 3){
1084	<	makeElement( i * cellx + 0.5 * cellx,
1085	<	j * celly,
1086	<	k * cellz + 0.5 * cellz );
1087	<	done = ( current_mol >= tot_nmol );
1088	<	}
1089	<	}
757	>	if (!done && n_per_extra > 3){
758	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
759	>	k * cellz + 0.5 * cellz);
760	>	done = (current_mol >= tot_nmol);
761	>	}
762	>	}
763		}
764		}
765		}
766
767	<
768	<	for( i=0; i<simnfo->n_atoms; i++ ){
1096	<	simnfo->atoms[i]->set_vx( 0.0 );
1097	<	simnfo->atoms[i]->set_vy( 0.0 );
1098	<	simnfo->atoms[i]->set_vz( 0.0 );
767	>	for (i = 0; i < info[0].n_atoms; i++){
768	>	info[0].atoms[i]->setVel(vel);
769		}
770		}
771
772	<	void SimSetup::makeElement( double x, double y, double z ){
1103	<
772	>	void SimSetup::makeElement(double x, double y, double z){
773		int k;
774		AtomStamp* current_atom;
775		DirectionalAtom* dAtom;
776		double rotMat[3][3];
777	+	double pos[3];
778
779	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
780	<
781	<	current_atom = comp_stamps[current_comp]->getAtom( k );
782	<	if( !current_atom->havePosition() ){
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup:initFromBass error.\n"
785	<	"\tComponent %s, atom %s does not have a position specified.\n"
786	<	"\tThe initialization routine is unable to give a start"
787	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
779	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
780	>	current_atom = comp_stamps[current_comp]->getAtom(k);
781	>	if (!current_atom->havePosition()){
782	>	sprintf(painCave.errMsg,
783	>	"SimSetup:initFromBass error.\n"
784	>	"\tComponent %s, atom %s does not have a position specified.\n"
785	>	"\tThe initialization routine is unable to give a start"
786	>	" position.\n",
787	>	comp_stamps[current_comp]->getID(), current_atom->getType());
788		painCave.isFatal = 1;
789		simError();
790		}
791
792	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
793	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
794	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
792	>	pos[0] = x + current_atom->getPosX();
793	>	pos[1] = y + current_atom->getPosY();
794	>	pos[2] = z + current_atom->getPosZ();
795
796	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
796	>	info[0].atoms[current_atom_ndx]->setPos(pos);
797
798	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
798	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
799	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
800
801		rotMat[0][0] = 1.0;
802		rotMat[0][1] = 0.0;
#	Line 1141 | Line 810 | void SimSetup::makeElement( double x, double y, double
810		rotMat[2][1] = 0.0;
811		rotMat[2][2] = 1.0;
812
813	<	dAtom->setA( rotMat );
813	>	dAtom->setA(rotMat);
814		}
815
816		current_atom_ndx++;
#	Line 1150 | Line 819 | void SimSetup::makeElement( double x, double y, double
819		current_mol++;
820		current_comp_mol++;
821
822	<	if( current_comp_mol >= components_nmol[current_comp] ){
1154	<
822	>	if (current_comp_mol >= components_nmol[current_comp]){
823		current_comp_mol = 0;
824		current_comp++;
825	+	}
826	+	}
827	+
828	+
829	+	void SimSetup::gatherInfo(void){
830	+	int i;
831	+
832	+	ensembleCase = -1;
833	+	ffCase = -1;
834	+
835	+	// set the easy ones first
836	+
837	+	for (i = 0; i < nInfo; i++){
838	+	info[i].target_temp = globals->getTargetTemp();
839	+	info[i].dt = globals->getDt();
840	+	info[i].run_time = globals->getRunTime();
841	+	}
842	+	n_components = globals->getNComponents();
843	+
844	+
845	+	// get the forceField
846	+
847	+	strcpy(force_field, globals->getForceField());
848	+
849	+	if (!strcasecmp(force_field, "DUFF")){
850	+	ffCase = FF_DUFF;
851	+	}
852	+	else if (!strcasecmp(force_field, "LJ")){
853	+	ffCase = FF_LJ;
854	+	}
855	+	else if (!strcasecmp(force_field, "EAM")){
856	+	ffCase = FF_EAM;
857	+	}
858	+	else if (!strcasecmp(force_field, "WATER")){
859	+	ffCase = FF_H2O;
860	+	}
861	+	else{
862	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
863	+	force_field);
864	+	painCave.isFatal = 1;
865	+	simError();
866	+	}
867	+
868	+	// get the ensemble
869	+
870	+	strcpy(ensemble, globals->getEnsemble());
871	+
872	+	if (!strcasecmp(ensemble, "NVE")){
873	+	ensembleCase = NVE_ENS;
874	+	}
875	+	else if (!strcasecmp(ensemble, "NVT")){
876	+	ensembleCase = NVT_ENS;
877	+	}
878	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
879	+	ensembleCase = NPTi_ENS;
880	+	}
881	+	else if (!strcasecmp(ensemble, "NPTf")){
882	+	ensembleCase = NPTf_ENS;
883	+	}
884	+	else if (!strcasecmp(ensemble, "NPTxyz")){
885	+	ensembleCase = NPTxyz_ENS;
886	+	}
887	+	else{
888	+	sprintf(painCave.errMsg,
889	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
890	+	"\treverting to NVE for this simulation.\n",
891	+	ensemble);
892	+	painCave.isFatal = 0;
893	+	simError();
894	+	strcpy(ensemble, "NVE");
895	+	ensembleCase = NVE_ENS;
896	+	}
897	+
898	+	for (i = 0; i < nInfo; i++){
899	+	strcpy(info[i].ensemble, ensemble);
900	+
901	+	// get the mixing rule
902	+
903	+	strcpy(info[i].mixingRule, globals->getMixingRule());
904	+	info[i].usePBC = globals->getPBC();
905	+	}
906	+
907	+	// get the components and calculate the tot_nMol and indvidual n_mol
908	+
909	+	the_components = globals->getComponents();
910	+	components_nmol = new int[n_components];
911	+
912	+
913	+	if (!globals->haveNMol()){
914	+	// we don't have the total number of molecules, so we assume it is
915	+	// given in each component
916	+
917	+	tot_nmol = 0;
918	+	for (i = 0; i < n_components; i++){
919	+	if (!the_components[i]->haveNMol()){
920	+	// we have a problem
921	+	sprintf(painCave.errMsg,
922	+	"SimSetup Error. No global NMol or component NMol given.\n"
923	+	"\tCannot calculate the number of atoms.\n");
924	+	painCave.isFatal = 1;
925	+	simError();
926	+	}
927	+
928	+	tot_nmol += the_components[i]->getNMol();
929	+	components_nmol[i] = the_components[i]->getNMol();
930	+	}
931	+	}
932	+	else{
933	+	sprintf(painCave.errMsg,
934	+	"SimSetup error.\n"
935	+	"\tSorry, the ability to specify total"
936	+	" nMols and then give molfractions in the components\n"
937	+	"\tis not currently supported."
938	+	" Please give nMol in the components.\n");
939	+	painCave.isFatal = 1;
940	+	simError();
941	+	}
942	+
943	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
944	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945	+	sprintf(painCave.errMsg,
946	+	"Sample time is not divisible by dt.\n"
947	+	"\tThis will result in samples that are not uniformly\n"
948	+	"\tdistributed in time.  If this is a problem, change\n"
949	+	"\tyour sampleTime variable.\n");
950	+	painCave.isFatal = 0;
951	+	simError();
952	+	}
953	+
954	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955	+	sprintf(painCave.errMsg,
956	+	"Status time is not divisible by dt.\n"
957	+	"\tThis will result in status reports that are not uniformly\n"
958	+	"\tdistributed in time.  If this is a problem, change \n"
959	+	"\tyour statusTime variable.\n");
960	+	painCave.isFatal = 0;
961	+	simError();
962	+	}
963	+
964	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
965	+	sprintf(painCave.errMsg,
966	+	"Thermal time is not divisible by dt.\n"
967	+	"\tThis will result in thermalizations that are not uniformly\n"
968	+	"\tdistributed in time.  If this is a problem, change \n"
969	+	"\tyour thermalTime variable.\n");
970	+	painCave.isFatal = 0;
971	+	simError();
972	+	}
973	+
974	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
975	+	sprintf(painCave.errMsg,
976	+	"Reset time is not divisible by dt.\n"
977	+	"\tThis will result in integrator resets that are not uniformly\n"
978	+	"\tdistributed in time.  If this is a problem, change\n"
979	+	"\tyour resetTime variable.\n");
980	+	painCave.isFatal = 0;
981	+	simError();
982	+	}
983	+
984	+	// set the status, sample, and thermal kick times
985	+
986	+	for (i = 0; i < nInfo; i++){
987	+	if (globals->haveSampleTime()){
988	+	info[i].sampleTime = globals->getSampleTime();
989	+	info[i].statusTime = info[i].sampleTime;
990	+	}
991	+	else{
992	+	info[i].sampleTime = globals->getRunTime();
993	+	info[i].statusTime = info[i].sampleTime;
994	+	}
995	+
996	+	if (globals->haveStatusTime()){
997	+	info[i].statusTime = globals->getStatusTime();
998	+	}
999	+
1000	+	if (globals->haveThermalTime()){
1001	+	info[i].thermalTime = globals->getThermalTime();
1002	+	} else {
1003	+	info[i].thermalTime = globals->getRunTime();
1004	+	}
1005	+
1006	+	info[i].resetIntegrator = 0;
1007	+	if( globals->haveResetTime() ){
1008	+	info[i].resetTime = globals->getResetTime();
1009	+	info[i].resetIntegrator = 1;
1010	+	}
1011	+
1012	+	// check for the temperature set flag
1013	+
1014	+	if (globals->haveTempSet())
1015	+	info[i].setTemp = globals->getTempSet();
1016	+
1017	+	// check for the extended State init
1018	+
1019	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1020	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021	+
1022	+	// check for thermodynamic integration
1023	+	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1024	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	+	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1026	+	info[i].thermIntLambda = globals->getThermIntLambda();
1027	+	info[i].thermIntK = globals->getThermIntK();
1028	+
1029	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	+	info[i].restraint = myRestraint;
1031	+	}
1032	+	else {
1033	+	sprintf(painCave.errMsg,
1034	+	"SimSetup Error:\n"
1035	+	"\tKeyword useSolidThermInt was set to 'true' but\n"
1036	+	"\tthermodynamicIntegrationLambda (and/or\n"
1037	+	"\tthermodynamicIntegrationK) was not specified.\n"
1038	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	+	painCave.isFatal = 1;
1040	+	simError();
1041	+	}
1042	+	}
1043	+	else if(globals->getUseLiquidThermInt()) {
1044	+	if (globals->getUseSolidThermInt()) {
1045	+	sprintf( painCave.errMsg,
1046	+	"SimSetup Warning: It appears that you have both solid and\n"
1047	+	"\tliquid thermodynamic integration activated in your .bass\n"
1048	+	"\tfile. To avoid confusion, specify only one technique in\n"
1049	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1050	+	"\twill be assumed for the current simulation. If this is not\n"
1051	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1052	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1053	+	painCave.isFatal = 0;
1054	+	simError();
1055	+	}
1056	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1057	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1058	+	info[i].thermIntLambda = globals->getThermIntLambda();
1059	+	info[i].thermIntK = globals->getThermIntK();
1060	+	}
1061	+	else {
1062	+	sprintf(painCave.errMsg,
1063	+	"SimSetup Error:\n"
1064	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1065	+	"\tthermodynamicIntegrationLambda (and/or\n"
1066	+	"\tthermodynamicIntegrationK) was not specified.\n"
1067	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1068	+	painCave.isFatal = 1;
1069	+	simError();
1070	+	}
1071	+	}
1072	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1073	+	sprintf(painCave.errMsg,
1074	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1075	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1076	+	"\t'true' in your .bass file.  These keywords are set to\n"
1077	+	"\t'false' by default, so your lambda and/or k values are\n"
1078	+	"\tbeing ignored.\n");
1079	+	painCave.isFatal = 0;
1080	+	simError();
1081	+	}
1082	+	}
1083	+
1084	+	//setup seed for random number generator
1085	+	int seedValue;
1086	+
1087	+	if (globals->haveSeed()){
1088	+	seedValue = globals->getSeed();
1089	+
1090	+	if(seedValue / 1E9 == 0){
1091	+	sprintf(painCave.errMsg,
1092	+	"Seed for sprng library should contain at least 9 digits\n"
1093	+	"OOPSE will generate a seed for user\n");
1094	+	painCave.isFatal = 0;
1095	+	simError();
1096	+
1097	+	//using seed generated by system instead of invalid seed set by user
1098	+	#ifndef IS_MPI
1099	+	seedValue = make_sprng_seed();
1100	+	#else
1101	+	if (worldRank == 0){
1102	+	seedValue = make_sprng_seed();
1103	+	}
1104	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1105	+	#endif
1106	+	}
1107	+	}//end of if branch of globals->haveSeed()
1108	+	else{
1109	+
1110	+	#ifndef IS_MPI
1111	+	seedValue = make_sprng_seed();
1112	+	#else
1113	+	if (worldRank == 0){
1114	+	seedValue = make_sprng_seed();
1115	+	}
1116	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1117	+	#endif
1118	+	}//end of globals->haveSeed()
1119	+
1120	+	for (int i = 0; i < nInfo; i++){
1121	+	info[i].setSeed(seedValue);
1122	+	}
1123	+
1124	+	#ifdef IS_MPI
1125	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1126	+	MPIcheckPoint();
1127	+	#endif // is_mpi
1128	+	}
1129	+
1130	+
1131	+	void SimSetup::finalInfoCheck(void){
1132	+	int index;
1133	+	int usesDipoles;
1134	+	int usesCharges;
1135	+	int i;
1136	+
1137	+	for (i = 0; i < nInfo; i++){
1138	+	// check electrostatic parameters
1139	+
1140	+	index = 0;
1141	+	usesDipoles = 0;
1142	+	while ((index < info[i].n_atoms) && !usesDipoles){
1143	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1144	+	index++;
1145	+	}
1146	+	index = 0;
1147	+	usesCharges = 0;
1148	+	while ((index < info[i].n_atoms) && !usesCharges){
1149	+	usesCharges= (info[i].atoms[index])->hasCharge();
1150	+	index++;
1151	+	}
1152	+	#ifdef IS_MPI
1153	+	int myUse = usesDipoles;
1154	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155	+	#endif //is_mpi
1156	+
1157	+	double theRcut, theRsw;
1158	+
1159	+	if (globals->haveRcut()) {
1160	+	theRcut = globals->getRcut();
1161	+
1162	+	if (globals->haveRsw())
1163	+	theRsw = globals->getRsw();
1164	+	else
1165	+	theRsw = theRcut;
1166	+
1167	+	info[i].setDefaultRcut(theRcut, theRsw);
1168	+
1169	+	} else {
1170	+
1171	+	the_ff->calcRcut();
1172	+	theRcut = info[i].getRcut();
1173	+
1174	+	if (globals->haveRsw())
1175	+	theRsw = globals->getRsw();
1176	+	else
1177	+	theRsw = theRcut;
1178	+
1179	+	info[i].setDefaultRcut(theRcut, theRsw);
1180	+	}
1181	+
1182	+	if (globals->getUseRF()){
1183	+	info[i].useReactionField = 1;
1184	+
1185	+	if (!globals->haveRcut()){
1186	+	sprintf(painCave.errMsg,
1187	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1188	+	"\tOOPSE will use a default value of 15.0 angstroms"
1189	+	"\tfor the cutoffRadius.\n");
1190	+	painCave.isFatal = 0;
1191	+	simError();
1192	+	theRcut = 15.0;
1193	+	}
1194	+	else{
1195	+	theRcut = globals->getRcut();
1196	+	}
1197	+
1198	+	if (!globals->haveRsw()){
1199	+	sprintf(painCave.errMsg,
1200	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1201	+	"\tOOPSE will use a default value of\n"
1202	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1203	+	painCave.isFatal = 0;
1204	+	simError();
1205	+	theRsw = 0.95 * theRcut;
1206	+	}
1207	+	else{
1208	+	theRsw = globals->getRsw();
1209	+	}
1210	+
1211	+	info[i].setDefaultRcut(theRcut, theRsw);
1212	+
1213	+	if (!globals->haveDielectric()){
1214	+	sprintf(painCave.errMsg,
1215	+	"SimSetup Error: No Dielectric constant was set.\n"
1216	+	"\tYou are trying to use Reaction Field without"
1217	+	"\tsetting a dielectric constant!\n");
1218	+	painCave.isFatal = 1;
1219	+	simError();
1220	+	}
1221	+	info[i].dielectric = globals->getDielectric();
1222	+	}
1223	+	else{
1224	+	if (usesDipoles || usesCharges){
1225	+
1226	+	if (!globals->haveRcut()){
1227	+	sprintf(painCave.errMsg,
1228	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	+	"\tOOPSE will use a default value of 15.0 angstroms"
1230	+	"\tfor the cutoffRadius.\n");
1231	+	painCave.isFatal = 0;
1232	+	simError();
1233	+	theRcut = 15.0;
1234	+	}
1235	+	else{
1236	+	theRcut = globals->getRcut();
1237	+	}
1238	+
1239	+	if (!globals->haveRsw()){
1240	+	sprintf(painCave.errMsg,
1241	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	+	"\tOOPSE will use a default value of\n"
1243	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	+	painCave.isFatal = 0;
1245	+	simError();
1246	+	theRsw = 0.95 * theRcut;
1247	+	}
1248	+	else{
1249	+	theRsw = globals->getRsw();
1250	+	}
1251	+
1252	+	info[i].setDefaultRcut(theRcut, theRsw);
1253	+
1254	+	}
1255	+	}
1256	+	}
1257	+	#ifdef IS_MPI
1258	+	strcpy(checkPointMsg, "post processing checks out");
1259	+	MPIcheckPoint();
1260	+	#endif // is_mpi
1261	+
1262	+	// clean up the forcefield
1263	+	the_ff->cleanMe();
1264	+	}
1265	+
1266	+	void SimSetup::initSystemCoords(void){
1267	+	int i;
1268	+
1269	+	char* inName;
1270	+
1271	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1272	+
1273	+	for (i = 0; i < info[0].n_atoms; i++)
1274	+	info[0].atoms[i]->setCoords();
1275	+
1276	+	if (globals->haveInitialConfig()){
1277	+	InitializeFromFile* fileInit;
1278	+	#ifdef IS_MPI // is_mpi
1279	+	if (worldRank == 0){
1280	+	#endif //is_mpi
1281	+	inName = globals->getInitialConfig();
1282	+	fileInit = new InitializeFromFile(inName);
1283	+	#ifdef IS_MPI
1284	+	}
1285	+	else
1286	+	fileInit = new InitializeFromFile(NULL);
1287	+	#endif
1288	+	fileInit->readInit(info); // default velocities on
1289	+
1290	+	delete fileInit;
1291		}
1292	+	else{
1293	+
1294	+	// no init from bass
1295	+
1296	+	sprintf(painCave.errMsg,
1297	+	"Cannot intialize a simulation without an initial configuration file.\n");
1298	+	painCave.isFatal = 1;;
1299	+	simError();
1300	+
1301	+	}
1302	+
1303	+	#ifdef IS_MPI
1304	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1305	+	MPIcheckPoint();
1306	+	#endif // is_mpi
1307		}
1308	+
1309	+
1310	+	void SimSetup::makeOutNames(void){
1311	+	int k;
1312	+
1313	+
1314	+	for (k = 0; k < nInfo; k++){
1315	+	#ifdef IS_MPI
1316	+	if (worldRank == 0){
1317	+	#endif // is_mpi
1318	+
1319	+	if (globals->haveFinalConfig()){
1320	+	strcpy(info[k].finalName, globals->getFinalConfig());
1321	+	}
1322	+	else{
1323	+	strcpy(info[k].finalName, inFileName);
1324	+	char* endTest;
1325	+	int nameLength = strlen(info[k].finalName);
1326	+	endTest = &(info[k].finalName[nameLength - 5]);
1327	+	if (!strcmp(endTest, ".bass")){
1328	+	strcpy(endTest, ".eor");
1329	+	}
1330	+	else if (!strcmp(endTest, ".BASS")){
1331	+	strcpy(endTest, ".eor");
1332	+	}
1333	+	else{
1334	+	endTest = &(info[k].finalName[nameLength - 4]);
1335	+	if (!strcmp(endTest, ".bss")){
1336	+	strcpy(endTest, ".eor");
1337	+	}
1338	+	else if (!strcmp(endTest, ".mdl")){
1339	+	strcpy(endTest, ".eor");
1340	+	}
1341	+	else{
1342	+	strcat(info[k].finalName, ".eor");
1343	+	}
1344	+	}
1345	+	}
1346	+
1347	+	// make the sample and status out names
1348	+
1349	+	strcpy(info[k].sampleName, inFileName);
1350	+	char* endTest;
1351	+	int nameLength = strlen(info[k].sampleName);
1352	+	endTest = &(info[k].sampleName[nameLength - 5]);
1353	+	if (!strcmp(endTest, ".bass")){
1354	+	strcpy(endTest, ".dump");
1355	+	}
1356	+	else if (!strcmp(endTest, ".BASS")){
1357	+	strcpy(endTest, ".dump");
1358	+	}
1359	+	else{
1360	+	endTest = &(info[k].sampleName[nameLength - 4]);
1361	+	if (!strcmp(endTest, ".bss")){
1362	+	strcpy(endTest, ".dump");
1363	+	}
1364	+	else if (!strcmp(endTest, ".mdl")){
1365	+	strcpy(endTest, ".dump");
1366	+	}
1367	+	else{
1368	+	strcat(info[k].sampleName, ".dump");
1369	+	}
1370	+	}
1371	+
1372	+	strcpy(info[k].statusName, inFileName);
1373	+	nameLength = strlen(info[k].statusName);
1374	+	endTest = &(info[k].statusName[nameLength - 5]);
1375	+	if (!strcmp(endTest, ".bass")){
1376	+	strcpy(endTest, ".stat");
1377	+	}
1378	+	else if (!strcmp(endTest, ".BASS")){
1379	+	strcpy(endTest, ".stat");
1380	+	}
1381	+	else{
1382	+	endTest = &(info[k].statusName[nameLength - 4]);
1383	+	if (!strcmp(endTest, ".bss")){
1384	+	strcpy(endTest, ".stat");
1385	+	}
1386	+	else if (!strcmp(endTest, ".mdl")){
1387	+	strcpy(endTest, ".stat");
1388	+	}
1389	+	else{
1390	+	strcat(info[k].statusName, ".stat");
1391	+	}
1392	+	}
1393	+
1394	+	strcpy(info[k].rawPotName, inFileName);
1395	+	nameLength = strlen(info[k].rawPotName);
1396	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1397	+	if (!strcmp(endTest, ".bass")){
1398	+	strcpy(endTest, ".raw");
1399	+	}
1400	+	else if (!strcmp(endTest, ".BASS")){
1401	+	strcpy(endTest, ".raw");
1402	+	}
1403	+	else{
1404	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1405	+	if (!strcmp(endTest, ".bss")){
1406	+	strcpy(endTest, ".raw");
1407	+	}
1408	+	else if (!strcmp(endTest, ".mdl")){
1409	+	strcpy(endTest, ".raw");
1410	+	}
1411	+	else{
1412	+	strcat(info[k].rawPotName, ".raw");
1413	+	}
1414	+	}
1415	+
1416	+	#ifdef IS_MPI
1417	+
1418	+	}
1419	+	#endif // is_mpi
1420	+	}
1421	+	}
1422	+
1423	+
1424	+	void SimSetup::sysObjectsCreation(void){
1425	+	int i, k;
1426	+
1427	+	// create the forceField
1428	+
1429	+	createFF();
1430	+
1431	+	// extract componentList
1432	+
1433	+	compList();
1434	+
1435	+	// calc the number of atoms, bond, bends, and torsions
1436	+
1437	+	calcSysValues();
1438	+
1439	+	#ifdef IS_MPI
1440	+	// divide the molecules among the processors
1441	+
1442	+	mpiMolDivide();
1443	+	#endif //is_mpi
1444	+
1445	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1446	+
1447	+	makeSysArrays();
1448	+
1449	+	// make and initialize the molecules (all but atomic coordinates)
1450	+
1451	+	makeMolecules();
1452	+
1453	+	for (k = 0; k < nInfo; k++){
1454	+	info[k].identArray = new int[info[k].n_atoms];
1455	+	for (i = 0; i < info[k].n_atoms; i++){
1456	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1457	+	}
1458	+	}
1459	+	}
1460	+
1461	+
1462	+	void SimSetup::createFF(void){
1463	+	switch (ffCase){
1464	+	case FF_DUFF:
1465	+	the_ff = new DUFF();
1466	+	break;
1467	+
1468	+	case FF_LJ:
1469	+	the_ff = new LJFF();
1470	+	break;
1471	+
1472	+	case FF_EAM:
1473	+	the_ff = new EAM_FF();
1474	+	break;
1475	+
1476	+	case FF_H2O:
1477	+	the_ff = new WATER();
1478	+	break;
1479	+
1480	+	default:
1481	+	sprintf(painCave.errMsg,
1482	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1483	+	painCave.isFatal = 1;
1484	+	simError();
1485	+	}
1486	+
1487	+	#ifdef IS_MPI
1488	+	strcpy(checkPointMsg, "ForceField creation successful");
1489	+	MPIcheckPoint();
1490	+	#endif // is_mpi
1491	+	}
1492	+
1493	+
1494	+	void SimSetup::compList(void){
1495	+	int i;
1496	+	char* id;
1497	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1498	+	LinkedMolStamp* currentStamp = NULL;
1499	+	comp_stamps = new MoleculeStamp * [n_components];
1500	+	bool haveCutoffGroups;
1501	+
1502	+	haveCutoffGroups = false;
1503	+
1504	+	// make an array of molecule stamps that match the components used.
1505	+	// also extract the used stamps out into a separate linked list
1506	+
1507	+	for (i = 0; i < nInfo; i++){
1508	+	info[i].nComponents = n_components;
1509	+	info[i].componentsNmol = components_nmol;
1510	+	info[i].compStamps = comp_stamps;
1511	+	info[i].headStamp = headStamp;
1512	+	}
1513	+
1514	+
1515	+	for (i = 0; i < n_components; i++){
1516	+	id = the_components[i]->getType();
1517	+	comp_stamps[i] = NULL;
1518	+
1519	+	// check to make sure the component isn't already in the list
1520	+
1521	+	comp_stamps[i] = headStamp->match(id);
1522	+	if (comp_stamps[i] == NULL){
1523	+	// extract the component from the list;
1524	+
1525	+	currentStamp = stamps->extractMolStamp(id);
1526	+	if (currentStamp == NULL){
1527	+	sprintf(painCave.errMsg,
1528	+	"SimSetup error: Component \"%s\" was not found in the "
1529	+	"list of declared molecules\n",
1530	+	id);
1531	+	painCave.isFatal = 1;
1532	+	simError();
1533	+	}
1534	+
1535	+	headStamp->add(currentStamp);
1536	+	comp_stamps[i] = headStamp->match(id);
1537	+	}
1538	+
1539	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1540	+	haveCutoffGroups = true;
1541	+	}
1542	+
1543	+	for (i = 0; i < nInfo; i++)
1544	+	info[i].haveCutoffGroups = haveCutoffGroups;
1545	+
1546	+	#ifdef IS_MPI
1547	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1548	+	MPIcheckPoint();
1549	+	#endif // is_mpi
1550	+	}
1551	+
1552	+	void SimSetup::calcSysValues(void){
1553	+	int i, j;
1554	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1555	+
1556	+	int* molMembershipArray;
1557	+	CutoffGroupStamp* cg;
1558	+
1559	+	tot_atoms = 0;
1560	+	tot_bonds = 0;
1561	+	tot_bends = 0;
1562	+	tot_torsions = 0;
1563	+	tot_rigid = 0;
1564	+	tot_groups = 0;
1565	+	for (i = 0; i < n_components; i++){
1566	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1567	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1568	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1569	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1570	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1571	+
1572	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1573	+	atomsingroups = 0;
1574	+	for (j=0; j < ncutgroups; j++) {
1575	+	cg = comp_stamps[i]->getCutoffGroup(j);
1576	+	atomsingroups += cg->getNMembers();
1577	+	}
1578	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1579	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1580	+	}
1581	+
1582	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1583	+	molMembershipArray = new int[tot_atoms];
1584	+
1585	+	for (i = 0; i < nInfo; i++){
1586	+	info[i].n_atoms = tot_atoms;
1587	+	info[i].n_bonds = tot_bonds;
1588	+	info[i].n_bends = tot_bends;
1589	+	info[i].n_torsions = tot_torsions;
1590	+	info[i].n_SRI = tot_SRI;
1591	+	info[i].n_mol = tot_nmol;
1592	+	info[i].ngroup = tot_groups;
1593	+	info[i].molMembershipArray = molMembershipArray;
1594	+	}
1595	+	}
1596	+
1597	+	#ifdef IS_MPI
1598	+
1599	+	void SimSetup::mpiMolDivide(void){
1600	+	int i, j, k;
1601	+	int localMol, allMol;
1602	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1603	+	int local_rigid, local_groups;
1604	+	vector<int> globalMolIndex;
1605	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1606	+	CutoffGroupStamp* cg;
1607	+
1608	+	mpiSim = new mpiSimulation(info);
1609	+
1610	+	mpiSim->divideLabor();
1611	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1612	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1613	+
1614	+	// set up the local variables
1615	+
1616	+	mol2proc = mpiSim->getMolToProcMap();
1617	+	molCompType = mpiSim->getMolComponentType();
1618	+
1619	+	allMol = 0;
1620	+	localMol = 0;
1621	+	local_atoms = 0;
1622	+	local_bonds = 0;
1623	+	local_bends = 0;
1624	+	local_torsions = 0;
1625	+	local_rigid = 0;
1626	+	local_groups = 0;
1627	+	globalAtomCounter = 0;
1628	+
1629	+	for (i = 0; i < n_components; i++){
1630	+	for (j = 0; j < components_nmol[i]; j++){
1631	+	if (mol2proc[allMol] == worldRank){
1632	+	local_atoms += comp_stamps[i]->getNAtoms();
1633	+	local_bonds += comp_stamps[i]->getNBonds();
1634	+	local_bends += comp_stamps[i]->getNBends();
1635	+	local_torsions += comp_stamps[i]->getNTorsions();
1636	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1637	+
1638	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1639	+	atomsingroups = 0;
1640	+	for (k=0; k < ncutgroups; k++) {
1641	+	cg = comp_stamps[i]->getCutoffGroup(k);
1642	+	atomsingroups += cg->getNMembers();
1643	+	}
1644	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1645	+	ncutgroups;
1646	+	local_groups += ngroupsinstamp;
1647	+
1648	+	localMol++;
1649	+	}
1650	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1651	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1652	+	globalAtomCounter++;
1653	+	}
1654	+
1655	+	allMol++;
1656	+	}
1657	+	}
1658	+	local_SRI = local_bonds + local_bends + local_torsions;
1659	+
1660	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1661	+
1662	+	if (local_atoms != info[0].n_atoms){
1663	+	sprintf(painCave.errMsg,
1664	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1665	+	"\tlocalAtom (%d) are not equal.\n",
1666	+	info[0].n_atoms, local_atoms);
1667	+	painCave.isFatal = 1;
1668	+	simError();
1669	+	}
1670	+
1671	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1672	+	if (local_groups != info[0].ngroup){
1673	+	sprintf(painCave.errMsg,
1674	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1675	+	"\tlocalGroups (%d) are not equal.\n",
1676	+	info[0].ngroup, local_groups);
1677	+	painCave.isFatal = 1;
1678	+	simError();
1679	+	}
1680	+
1681	+	info[0].n_bonds = local_bonds;
1682	+	info[0].n_bends = local_bends;
1683	+	info[0].n_torsions = local_torsions;
1684	+	info[0].n_SRI = local_SRI;
1685	+	info[0].n_mol = localMol;
1686	+
1687	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1688	+	MPIcheckPoint();
1689	+	}
1690	+
1691	+	#endif // is_mpi
1692	+
1693	+
1694	+	void SimSetup::makeSysArrays(void){
1695	+
1696	+	#ifndef IS_MPI
1697	+	int k, j;
1698	+	#endif // is_mpi
1699	+	int i, l;
1700	+
1701	+	Atom** the_atoms;
1702	+	Molecule* the_molecules;
1703	+
1704	+	for (l = 0; l < nInfo; l++){
1705	+	// create the atom and short range interaction arrays
1706	+
1707	+	the_atoms = new Atom * [info[l].n_atoms];
1708	+	the_molecules = new Molecule[info[l].n_mol];
1709	+	int molIndex;
1710	+
1711	+	// initialize the molecule's stampID's
1712	+
1713	+	#ifdef IS_MPI
1714	+
1715	+
1716	+	molIndex = 0;
1717	+	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1718	+	if (mol2proc[i] == worldRank){
1719	+	the_molecules[molIndex].setStampID(molCompType[i]);
1720	+	the_molecules[molIndex].setMyIndex(molIndex);
1721	+	the_molecules[molIndex].setGlobalIndex(i);
1722	+	molIndex++;
1723	+	}
1724	+	}
1725	+
1726	+	#else // is_mpi
1727	+
1728	+	molIndex = 0;
1729	+	globalAtomCounter = 0;
1730	+	for (i = 0; i < n_components; i++){
1731	+	for (j = 0; j < components_nmol[i]; j++){
1732	+	the_molecules[molIndex].setStampID(i);
1733	+	the_molecules[molIndex].setMyIndex(molIndex);
1734	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1735	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1736	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1737	+	globalAtomCounter++;
1738	+	}
1739	+	molIndex++;
1740	+	}
1741	+	}
1742	+
1743	+
1744	+	#endif // is_mpi
1745	+
1746	+	info[l].globalExcludes = new int;
1747	+	info[l].globalExcludes[0] = 0;
1748	+
1749	+	// set the arrays into the SimInfo object
1750	+
1751	+	info[l].atoms = the_atoms;
1752	+	info[l].molecules = the_molecules;
1753	+	info[l].nGlobalExcludes = 0;
1754	+
1755	+	the_ff->setSimInfo(info);
1756	+	}
1757	+	}
1758	+
1759	+	void SimSetup::makeIntegrator(void){
1760	+	int k;
1761	+
1762	+	NVE<RealIntegrator>* myNVE = NULL;
1763	+	NVT<RealIntegrator>* myNVT = NULL;
1764	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1765	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1766	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1767	+
1768	+	for (k = 0; k < nInfo; k++){
1769	+	switch (ensembleCase){
1770	+	case NVE_ENS:
1771	+	if (globals->haveZconstraints()){
1772	+	setupZConstraint(info[k]);
1773	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1774	+	}
1775	+	else{
1776	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1777	+	}
1778	+
1779	+	info->the_integrator = myNVE;
1780	+	break;
1781	+
1782	+	case NVT_ENS:
1783	+	if (globals->haveZconstraints()){
1784	+	setupZConstraint(info[k]);
1785	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1786	+	}
1787	+	else
1788	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1789	+
1790	+	myNVT->setTargetTemp(globals->getTargetTemp());
1791	+
1792	+	if (globals->haveTauThermostat())
1793	+	myNVT->setTauThermostat(globals->getTauThermostat());
1794	+	else{
1795	+	sprintf(painCave.errMsg,
1796	+	"SimSetup error: If you use the NVT\n"
1797	+	"\tensemble, you must set tauThermostat.\n");
1798	+	painCave.isFatal = 1;
1799	+	simError();
1800	+	}
1801	+
1802	+	info->the_integrator = myNVT;
1803	+	break;
1804	+
1805	+	case NPTi_ENS:
1806	+	if (globals->haveZconstraints()){
1807	+	setupZConstraint(info[k]);
1808	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1809	+	}
1810	+	else
1811	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1812	+
1813	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1814	+
1815	+	if (globals->haveTargetPressure())
1816	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1817	+	else{
1818	+	sprintf(painCave.errMsg,
1819	+	"SimSetup error: If you use a constant pressure\n"
1820	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1821	+	painCave.isFatal = 1;
1822	+	simError();
1823	+	}
1824	+
1825	+	if (globals->haveTauThermostat())
1826	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1827	+	else{
1828	+	sprintf(painCave.errMsg,
1829	+	"SimSetup error: If you use an NPT\n"
1830	+	"\tensemble, you must set tauThermostat.\n");
1831	+	painCave.isFatal = 1;
1832	+	simError();
1833	+	}
1834	+
1835	+	if (globals->haveTauBarostat())
1836	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1837	+	else{
1838	+	sprintf(painCave.errMsg,
1839	+	"SimSetup error: If you use an NPT\n"
1840	+	"\tensemble, you must set tauBarostat.\n");
1841	+	painCave.isFatal = 1;
1842	+	simError();
1843	+	}
1844	+
1845	+	info->the_integrator = myNPTi;
1846	+	break;
1847	+
1848	+	case NPTf_ENS:
1849	+	if (globals->haveZconstraints()){
1850	+	setupZConstraint(info[k]);
1851	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1852	+	}
1853	+	else
1854	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1855	+
1856	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1857	+
1858	+	if (globals->haveTargetPressure())
1859	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1860	+	else{
1861	+	sprintf(painCave.errMsg,
1862	+	"SimSetup error: If you use a constant pressure\n"
1863	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1864	+	painCave.isFatal = 1;
1865	+	simError();
1866	+	}
1867	+
1868	+	if (globals->haveTauThermostat())
1869	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1870	+
1871	+	else{
1872	+	sprintf(painCave.errMsg,
1873	+	"SimSetup error: If you use an NPT\n"
1874	+	"\tensemble, you must set tauThermostat.\n");
1875	+	painCave.isFatal = 1;
1876	+	simError();
1877	+	}
1878	+
1879	+	if (globals->haveTauBarostat())
1880	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1881	+
1882	+	else{
1883	+	sprintf(painCave.errMsg,
1884	+	"SimSetup error: If you use an NPT\n"
1885	+	"\tensemble, you must set tauBarostat.\n");
1886	+	painCave.isFatal = 1;
1887	+	simError();
1888	+	}
1889	+
1890	+	info->the_integrator = myNPTf;
1891	+	break;
1892	+
1893	+	case NPTxyz_ENS:
1894	+	if (globals->haveZconstraints()){
1895	+	setupZConstraint(info[k]);
1896	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	+	}
1898	+	else
1899	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	+
1901	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1902	+
1903	+	if (globals->haveTargetPressure())
1904	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1905	+	else{
1906	+	sprintf(painCave.errMsg,
1907	+	"SimSetup error: If you use a constant pressure\n"
1908	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1909	+	painCave.isFatal = 1;
1910	+	simError();
1911	+	}
1912	+
1913	+	if (globals->haveTauThermostat())
1914	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1915	+	else{
1916	+	sprintf(painCave.errMsg,
1917	+	"SimSetup error: If you use an NPT\n"
1918	+	"\tensemble, you must set tauThermostat.\n");
1919	+	painCave.isFatal = 1;
1920	+	simError();
1921	+	}
1922	+
1923	+	if (globals->haveTauBarostat())
1924	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1925	+	else{
1926	+	sprintf(painCave.errMsg,
1927	+	"SimSetup error: If you use an NPT\n"
1928	+	"\tensemble, you must set tauBarostat.\n");
1929	+	painCave.isFatal = 1;
1930	+	simError();
1931	+	}
1932	+
1933	+	info->the_integrator = myNPTxyz;
1934	+	break;
1935	+
1936	+	default:
1937	+	sprintf(painCave.errMsg,
1938	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1939	+	painCave.isFatal = 1;
1940	+	simError();
1941	+	}
1942	+	}
1943	+	}
1944	+
1945	+	void SimSetup::initFortran(void){
1946	+	info[0].refreshSim();
1947	+
1948	+	if (!strcmp(info[0].mixingRule, "standard")){
1949	+	the_ff->initForceField(LB_MIXING_RULE);
1950	+	}
1951	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1952	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1953	+	}
1954	+	else{
1955	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1956	+	info[0].mixingRule);
1957	+	painCave.isFatal = 1;
1958	+	simError();
1959	+	}
1960	+
1961	+
1962	+	#ifdef IS_MPI
1963	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1964	+	MPIcheckPoint();
1965	+	#endif // is_mpi
1966	+	}
1967	+
1968	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1969	+	int nZConstraints;
1970	+	ZconStamp** zconStamp;
1971	+
1972	+	if (globals->haveZconstraintTime()){
1973	+	//add sample time of z-constraint  into SimInfo's property list
1974	+	DoubleData* zconsTimeProp = new DoubleData();
1975	+	zconsTimeProp->setID(ZCONSTIME_ID);
1976	+	zconsTimeProp->setData(globals->getZconsTime());
1977	+	theInfo.addProperty(zconsTimeProp);
1978	+	}
1979	+	else{
1980	+	sprintf(painCave.errMsg,
1981	+	"ZConstraint error: If you use a ZConstraint,\n"
1982	+	"\tyou must set zconsTime.\n");
1983	+	painCave.isFatal = 1;
1984	+	simError();
1985	+	}
1986	+
1987	+	//push zconsTol into siminfo, if user does not specify
1988	+	//value for zconsTol, a default value will be used
1989	+	DoubleData* zconsTol = new DoubleData();
1990	+	zconsTol->setID(ZCONSTOL_ID);
1991	+	if (globals->haveZconsTol()){
1992	+	zconsTol->setData(globals->getZconsTol());
1993	+	}
1994	+	else{
1995	+	double defaultZConsTol = 0.01;
1996	+	sprintf(painCave.errMsg,
1997	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1998	+	"\tOOPSE will use a default value of %f.\n"
1999	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2000	+	defaultZConsTol);
2001	+	painCave.isFatal = 0;
2002	+	simError();
2003	+
2004	+	zconsTol->setData(defaultZConsTol);
2005	+	}
2006	+	theInfo.addProperty(zconsTol);
2007	+
2008	+	//set Force Subtraction Policy
2009	+	StringData* zconsForcePolicy = new StringData();
2010	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2011	+
2012	+	if (globals->haveZconsForcePolicy()){
2013	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2014	+	}
2015	+	else{
2016	+	sprintf(painCave.errMsg,
2017	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2018	+	"\tOOPSE will use PolicyByMass.\n"
2019	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2020	+	painCave.isFatal = 0;
2021	+	simError();
2022	+	zconsForcePolicy->setData("BYMASS");
2023	+	}
2024	+
2025	+	theInfo.addProperty(zconsForcePolicy);
2026	+
2027	+	//set zcons gap
2028	+	DoubleData* zconsGap = new DoubleData();
2029	+	zconsGap->setID(ZCONSGAP_ID);
2030	+
2031	+	if (globals->haveZConsGap()){
2032	+	zconsGap->setData(globals->getZconsGap());
2033	+	theInfo.addProperty(zconsGap);
2034	+	}
2035	+
2036	+	//set zcons fixtime
2037	+	DoubleData* zconsFixtime = new DoubleData();
2038	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2039	+
2040	+	if (globals->haveZConsFixTime()){
2041	+	zconsFixtime->setData(globals->getZconsFixtime());
2042	+	theInfo.addProperty(zconsFixtime);
2043	+	}
2044	+
2045	+	//set zconsUsingSMD
2046	+	IntData* zconsUsingSMD = new IntData();
2047	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2048	+
2049	+	if (globals->haveZConsUsingSMD()){
2050	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2051	+	theInfo.addProperty(zconsUsingSMD);
2052	+	}
2053	+
2054	+	//Determine the name of ouput file and add it into SimInfo's property list
2055	+	//Be careful, do not use inFileName, since it is a pointer which
2056	+	//point to a string at master node, and slave nodes do not contain that string
2057	+
2058	+	string zconsOutput(theInfo.finalName);
2059	+
2060	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2061	+
2062	+	StringData* zconsFilename = new StringData();
2063	+	zconsFilename->setID(ZCONSFILENAME_ID);
2064	+	zconsFilename->setData(zconsOutput);
2065	+
2066	+	theInfo.addProperty(zconsFilename);
2067	+
2068	+	//setup index, pos and other parameters of z-constraint molecules
2069	+	nZConstraints = globals->getNzConstraints();
2070	+	theInfo.nZconstraints = nZConstraints;
2071	+
2072	+	zconStamp = globals->getZconStamp();
2073	+	ZConsParaItem tempParaItem;
2074	+
2075	+	ZConsParaData* zconsParaData = new ZConsParaData();
2076	+	zconsParaData->setID(ZCONSPARADATA_ID);
2077	+
2078	+	for (int i = 0; i < nZConstraints; i++){
2079	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2080	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2081	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2082	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2083	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2084	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2085	+	zconsParaData->addItem(tempParaItem);
2086	+	}
2087	+
2088	+	//check the uniqueness of index
2089	+	if(!zconsParaData->isIndexUnique()){
2090	+	sprintf(painCave.errMsg,
2091	+	"ZConstraint Error: molIndex is not unique!\n");
2092	+	painCave.isFatal = 1;
2093	+	simError();
2094	+	}
2095	+
2096	+	//sort the parameters by index of molecules
2097	+	zconsParaData->sortByIndex();
2098	+
2099	+	//push data into siminfo, therefore, we can retrieve later
2100	+	theInfo.addProperty(zconsParaData);
2101	+	}
2102	+
2103	+	void SimSetup::makeMinimizer(){
2104	+
2105	+	OOPSEMinimizer* myOOPSEMinimizer;
2106	+	MinimizerParameterSet* param;
2107	+	char minimizerName[100];
2108	+
2109	+	for (int i = 0; i < nInfo; i++){
2110	+
2111	+	//prepare parameter set for minimizer
2112	+	param = new MinimizerParameterSet();
2113	+	param->setDefaultParameter();
2114	+
2115	+	if (globals->haveMinimizer()){
2116	+	param->setFTol(globals->getMinFTol());
2117	+	}
2118	+
2119	+	if (globals->haveMinGTol()){
2120	+	param->setGTol(globals->getMinGTol());
2121	+	}
2122	+
2123	+	if (globals->haveMinMaxIter()){
2124	+	param->setMaxIteration(globals->getMinMaxIter());
2125	+	}
2126	+
2127	+	if (globals->haveMinWriteFrq()){
2128	+	param->setMaxIteration(globals->getMinMaxIter());
2129	+	}
2130	+
2131	+	if (globals->haveMinWriteFrq()){
2132	+	param->setWriteFrq(globals->getMinWriteFrq());
2133	+	}
2134	+
2135	+	if (globals->haveMinStepSize()){
2136	+	param->setStepSize(globals->getMinStepSize());
2137	+	}
2138	+
2139	+	if (globals->haveMinLSMaxIter()){
2140	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2141	+	}
2142	+
2143	+	if (globals->haveMinLSTol()){
2144	+	param->setLineSearchTol(globals->getMinLSTol());
2145	+	}
2146	+
2147	+	strcpy(minimizerName, globals->getMinimizer());
2148	+
2149	+	if (!strcasecmp(minimizerName, "CG")){
2150	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2151	+	}
2152	+	else if (!strcasecmp(minimizerName, "SD")){
2153	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2154	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2155	+	}
2156	+	else{
2157	+	sprintf(painCave.errMsg,
2158	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2159	+	painCave.isFatal = 0;
2160	+	simError();
2161	+
2162	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2163	+	}
2164	+	info[i].the_integrator = myOOPSEMinimizer;
2165	+
2166	+	//store the minimizer into simInfo
2167	+	info[i].the_minimizer = myOOPSEMinimizer;
2168	+	info[i].has_minimizer = true;
2169	+	}
2170	+
2171	+	}

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