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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 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	<
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146	>	}
147
148	<	// 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];
148	>	// make the output filenames
149
150	<	if( !the_globals->haveNMol() ){
151	<	// we don't have the total number of molecules, so we assume it is
152	<	// given in each component
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
156	>	// initialize the Fortran
157
158	<	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	<	}
158	>	initFortran();
159
160	<	tot_nmol += the_components[i]->getNMol();
161	<	components_nmol[i] = the_components[i]->getNMol();
162	<	}
163	<	}
164	<	else{
165	<	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	<	}
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
167	>	}
168
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
169
170	<	simnfo->nComponents = n_components;
171	<	simnfo->componentsNmol = components_nmol;
172	<	simnfo->compStamps = comp_stamps;
173	<	simnfo->headStamp = new LinkedMolStamp();
174	<
175	<	char* id;
176	<	LinkedMolStamp* headStamp = simnfo->headStamp;
177	<	LinkedMolStamp* currentStamp = NULL;
178	<	for( i=0; i<n_components; i++ ){
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, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
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	<	id = the_components[i]->getType();
193	<	comp_stamps[i] = NULL;
194	<
181	<	// check to make sure the component isn't already in the list
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
196	>	set<int> skipList;
197
198	<	#ifdef IS_MPI
199	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
200	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
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	+	the_ff->readParams();
211
212	<	// caclulate the number of atoms, bonds, bends and torsions
212	<
213	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
212	>	// init the atoms
213
214	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
214	>	int nMembers, nNew, rb1, rb2;
215
216	<	simnfo->n_atoms = tot_atoms;
217	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
234	–
219		#ifdef IS_MPI
220	+	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	+	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	+	info[k].globalGroupMembership[i] = 0;
223	+	#else
224	+	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	+	for (i = 0; i < info[k].n_atoms; i++)
226	+	info[k].globalGroupMembership[i] = 0;
227	+	#endif
228
229	<	// divide the molecules among processors here.
230	<
239	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
229	>	atomOffset = 0;
230	>	groupOffset = 0;
231
232	<	globalIndex = mpiSim->divideLabor();
232	>	for (i = 0; i < info[k].n_mol; i++){
233	>	stampID = info[k].molecules[i].getStampID();
234	>	molName = comp_stamps[stampID]->getID();
235
236	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
239	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	+	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	<
247	<	// set up the local variables
248	<
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++ ){
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
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	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246	<	simnfo->n_atoms = mpiSim->getMyNlocal();
247	<
248	<	if( local_atoms != simnfo->n_atoms ){
249	<	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	>	if (molInfo.nBonds > 0)
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	>	else
249	>	molInfo.myBonds = NULL;
250
251	<	simnfo->n_bonds = local_bonds;
252	<	simnfo->n_bends = local_bends;
253	<	simnfo->n_torsions = local_torsions;
254	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
251	>	if (molInfo.nBends > 0)
252	>	molInfo.myBends = new Bend*[molInfo.nBends];
253	>	else
254	>	molInfo.myBends = NULL;
255
256	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
257	<	MPIcheckPoint();
258	<
259	<
299	<	#endif // is_mpi
300	<
256	>	if (molInfo.nTorsions > 0)
257	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	>	else
259	>	molInfo.myTorsions = NULL;
260
261	<	// create the atom and short range interaction arrays
261	>	theBonds = new bond_pair[molInfo.nBonds];
262	>	theBends = new bend_set[molInfo.nBends];
263	>	theTorsions = new torsion_set[molInfo.nTorsions];
264	>
265	>	// make the Atoms
266
267	<	Atom::createArrays(simnfo->n_atoms);
268	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
267	>	for (j = 0; j < molInfo.nAtoms; j++){
268	>	currentAtom = comp_stamps[stampID]->getAtom(j);
269
270	+	if (currentAtom->haveOrientation()){
271	+	dAtom = new DirectionalAtom((j + atomOffset),
272	+	info[k].getConfiguration());
273	+	info[k].n_oriented++;
274	+	molInfo.myAtoms[j] = dAtom;
275
276	<	if( simnfo->n_SRI ){
277	<	the_sris = new SRI*[simnfo->n_SRI];
278	<	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;
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	simnfo->n_exclude = 1;
281	<	}
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	// set the arrays into the SimInfo object
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288
289	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	+	}
292
293	<	// get some of the tricky things that may still be in the globals
293	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
294	>	#ifdef IS_MPI
295	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296	>	#endif // is_mpi
297	>	}
298
299	<
300	<	if( the_globals->haveBox() ){
301	<	simnfo->box_x = the_globals->getBox();
302	<	simnfo->box_y = the_globals->getBox();
303	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
299	>	// make the bonds
300	>	for (j = 0; j < molInfo.nBonds; j++){
301	>	currentBond = comp_stamps[stampID]->getBond(j);
302	>	theBonds[j].a = currentBond->getA() + atomOffset;
303	>	theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	double vol;
306	<	vol = (double)tot_nmol / the_globals->getDensity();
346	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	<	simnfo->box_y = simnfo->box_x;
348	<	simnfo->box_z = simnfo->box_x;
349	<	}
350	<	else{
351	<	if( !the_globals->haveBoxX() ){
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup error, no periodic BoxX size given.\n" );
354	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
308		#ifdef IS_MPI
309	<	strcpy( checkPointMsg, "Box size set up" );
310	<	MPIcheckPoint();
311	<	#endif // is_mpi
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	+	info[k].excludes->addPair(exI, exJ);
317	+	}
318
319	<	// initialize the arrays
319	>	//make the bends
320	>	for (j = 0; j < molInfo.nBends; j++){
321	>	currentBend = comp_stamps[stampID]->getBend(j);
322	>	theBends[j].a = currentBend->getA() + atomOffset;
323	>	theBends[j].b = currentBend->getB() + atomOffset;
324	>	theBends[j].c = currentBend->getC() + atomOffset;
325
326	<	the_ff->setSimInfo( simnfo );
326	>	if (currentBend->haveExtras()){
327	>	extras = currentBend->getExtras();
328	>	current_extra = extras;
329
330	<	makeAtoms();
331	<	simnfo->identArray = new int[simnfo->n_atoms];
332	<	for(i=0; i<simnfo->n_atoms; i++){
333	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
334	<	}
335	<
336	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
330	>	while (current_extra != NULL){
331	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
332	>	switch (current_extra->getType()){
333	>	case 0:
334	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
335	>	theBends[j].isGhost = 1;
336	>	break;
337
338	<	if( tot_bends ){
339	<	makeBends();
340	<	}
338	>	case 1:
339	>	theBends[j].ghost = (int) current_extra->getDouble() +
340	>	atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343
344	<	if( tot_torsions ){
345	<	makeTorsions();
346	<	}
344	>	default:
345	>	sprintf(painCave.errMsg,
346	>	"SimSetup Error: ghostVectorSource was neither a "
347	>	"double nor an int.\n"
348	>	"-->Bend[%d] in %s\n",
349	>	j, comp_stamps[stampID]->getID());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353	>	}
354	>	else{
355	>	sprintf(painCave.errMsg,
356	>	"SimSetup Error: unhandled bend assignment:\n"
357	>	"    -->%s in Bend[%d] in %s\n",
358	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
359	>	painCave.isFatal = 1;
360	>	simError();
361	>	}
362
363	+	current_extra = current_extra->getNext();
364	+	}
365	+	}
366
367	<	if (the_globals->getUseRF() ) {
368	<	simnfo->useReactionField = 1;
369	<
370	<	if( !the_globals->haveECR() ){
371	<	sprintf( painCave.errMsg,
372	<	"SimSetup Warning: using default value of 1/2 the smallest "
373	<	"box length for the electrostaticCutoffRadius.\n"
374	<	"I hope you have a very fast processor!\n");
375	<	painCave.isFatal = 0;
376	<	simError();
377	<	double smallest;
378	<	smallest = simnfo->box_x;
379	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
367	>	if (theBends[j].isGhost) {
368	>
369	>	tempI = theBends[j].a;
370	>	tempJ = theBends[j].b;
371	>
372	>	#ifdef IS_MPI
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380
381	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
381	>	} else {
382
383	+	tempI = theBends[j].a;
384	+	tempJ = theBends[j].b;
385	+	tempK = theBends[j].c;
386	+
387		#ifdef IS_MPI
388	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
389	<	MPIcheckPoint();
390	<	#endif // is_mpi
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395	>	#endif
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401	>	}
402
403	<	if( the_globals->haveInitialConfig() ){
404	<
405	<	InitializeFromFile* fileInit;
406	<	#ifdef IS_MPI // is_mpi
407	<	if( worldRank == 0 ){
408	<	#endif //is_mpi
409	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
403	>	for (j = 0; j < molInfo.nTorsions; j++){
404	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
405	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
406	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
407	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
408	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
409	>
410	>	tempI = theTorsions[j].a;
411	>	tempJ = theTorsions[j].b;
412	>	tempK = theTorsions[j].c;
413	>	tempL = theTorsions[j].d;
414	>
415		#ifdef IS_MPI
416	<	}else fileInit = new InitializeFromFile( NULL );
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
426
427	<	delete fileInit;
428	<	}
429	<	else{
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434
435	<	#ifdef IS_MPI
435	>
436	>	molInfo.myRigidBodies.clear();
437	>
438	>	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	<	// no init from bass
441	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
440	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	>	nMembers = currentRigidBody->getNMembers();
442
443	<	initFromBass();
443	>	// Create the Rigid Body:
444
445	+	myRB = new RigidBody();
446
447	<	#endif
448	<	}
447	>	sprintf(rbName,"%s_RB_%d", molName, j);
448	>	myRB->setType(rbName);
449	>
450	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
451
452	<	#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454
455	+	// tempI is atom numbering on local processor
456	+	tempI = molI + atomOffset;
457
458	<
459	<
460	<
458	>	// currentAtom is the AtomStamp (which we need for
459	>	// rigid body reference positions)
460	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
461
462	<
462	>	// When we add to the rigid body, add the atom itself and
463	>	// the stamp info:
464	>
465	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	>
467	>	// Add this atom to the Skip List for the integrators
468		#ifdef IS_MPI
469	<	if( worldRank == 0 ){
470	<	#endif // is_mpi
471	<
472	<	if( the_globals->haveFinalConfig() ){
473	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
474	<	}
475	<	else{
476	<	strcpy( simnfo->finalName, inFileName );
477	<	char* endTest;
478	<	int nameLength = strlen( simnfo->finalName );
479	<	endTest = &(simnfo->finalName[nameLength - 5]);
480	<	if( !strcmp( endTest, ".bass" ) ){
481	<	strcpy( endTest, ".eor" );
482	<	}
483	<	else if( !strcmp( endTest, ".BASS" ) ){
484	<	strcpy( endTest, ".eor" );
485	<	}
486	<	else{
487	<	endTest = &(simnfo->finalName[nameLength - 4]);
548	<	if( !strcmp( endTest, ".bss" ) ){
549	<	strcpy( endTest, ".eor" );
550	<	}
551	<	else if( !strcmp( endTest, ".mdl" ) ){
552	<	strcpy( endTest, ".eor" );
553	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
469	>	slI = info[k].atoms[tempI]->getGlobalIndex();
470	>	#else
471	>	slI = tempI;
472	>	#endif
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488		#ifdef IS_MPI
489	<	}
490	<	#endif // is_mpi
491	<
492	<	// set the status, sample, and themal kick times
493	<
494	<	if( the_globals->haveSampleTime() ){
495	<	simnfo->sampleTime = the_globals->getSampleTime();
496	<	simnfo->statusTime = simnfo->sampleTime;
497	<	simnfo->thermalTime = simnfo->sampleTime;
498	<	}
499	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500
501	<	if( the_globals->haveStatusTime() ){
502	<	simnfo->statusTime = the_globals->getStatusTime();
503	<	}
501	>	molInfo.myRigidBodies.push_back(myRB);
502	>	info[k].rigidBodies.push_back(myRB);
503	>	}
504	>
505
506	<	if( the_globals->haveThermalTime() ){
629	<	simnfo->thermalTime = the_globals->getThermalTime();
630	<	}
506	>	//create cutoff group for molecule
507
508	<	// check for the temperature set flag
508	>	cutoffAtomSet.clear();
509	>	molInfo.myCutoffGroups.clear();
510	>
511	>	for (j = 0; j < nCutoffGroups; j++){
512
513	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
513	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	>	nMembers = currentCutoffGroup->getNMembers();
515
516	+	myCutoffGroup = new CutoffGroup();
517	+
518	+	#ifdef IS_MPI
519	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
520	+	#else
521	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
522	+	#endif
523	+
524	+	for (int cg = 0; cg < nMembers; cg++) {
525
526	<	//   // make the longe range forces and the integrator
526	>	// molI is atom numbering inside this molecule
527	>	molI = currentCutoffGroup->getMember(cg);
528
529	<	//   new AllLong( simnfo );
529	>	// tempI is atom numbering on local processor
530	>	tempI = molI + atomOffset;
531
532	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
533	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
534	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
535	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
532	>	#ifdef IS_MPI
533	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = j + groupOffset;
538	>	#endif
539	>
540
541	+
542	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
543	+
544	+	cutoffAtomSet.insert(tempI);
545	+	}
546	+
547	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
548	+	groupOffset++;
549
550	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551	+
552	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
553	+
554	+	for(j = 0; j < molInfo.nAtoms; j++){
555	+
556	+	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557	+	myCutoffGroup = new CutoffGroup();
558	+	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559
560	<	// initialize the Fortran
561	<
562	<	simnfo->refreshSim();
563	<
564	<	if( !strcmp( simnfo->mixingRule, "standard") ){
565	<	the_ff->initForceField( LB_MIXING_RULE );
566	<	}
567	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
568	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
569	<	}
570	<	else{
571	<	sprintf( painCave.errMsg,
572	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
573	<	simnfo->mixingRule );
662	<	painCave.isFatal = 1;
663	<	simError();
664	<	}
560	>	#ifdef IS_MPI
561	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564	>	#else
565	>	myCutoffGroup->setGlobalIndex(j + groupOffset);
566	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
567	>	info[k].globalGroupMembership[globalID] = j+groupOffset;
568	>	#endif
569	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
570	>	groupOffset++;
571	>	}
572	>
573	>	}
574
575	+	// After this is all set up, scan through the atoms to
576	+	// see if they can be added to the integrableObjects:
577
578	+	molInfo.myIntegrableObjects.clear();
579	+
580	+
581	+	for (j = 0; j < molInfo.nAtoms; j++){
582	+
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg,
585	<	"Successfully intialized the mixingRule for Fortran." );
586	<	MPIcheckPoint();
587	<	#endif // is_mpi
672	<	}
584	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
585	>	#else
586	>	slJ = j+atomOffset;
587	>	#endif
588
589	+	// if they aren't on the skip list, then they can be integrated
590
591	<	void SimSetup::makeMolecules( void ){
591	>	if (skipList.find(slJ) == skipList.end()) {
592	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
593	>	info[k].integrableObjects.push_back(mySD);
594	>	molInfo.myIntegrableObjects.push_back(mySD);
595	>	}
596	>	}
597
598	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
684	<
685	<	//init the forceField paramters
598	>	// all rigid bodies are integrated:
599
600	<	the_ff->readParams();
600	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
601	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
602	>	info[k].integrableObjects.push_back(mySD);
603	>	molInfo.myIntegrableObjects.push_back(mySD);
604	>	}
605
689	–
690	–	// init the molecules
606
607	<	atomOffset = 0;
693	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
607	>	/*
608
609	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
610	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	<	info.nBends    = comp_stamps[stampID]->getNBends();
700	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	<
702	<	info.myAtoms = &the_atoms[atomOffset];
703	<	info.myBonds = new Bond*[info.nBonds];
704	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
706	<
707	<	theBonds = new bond_pair[info.nBonds];
708	<	theBends = new bend_set[info.nBends];
709	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
609	>	//creat ConstraintPair.
610	>	molInfo.myConstraintPair.clear();
611
612	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
736	<	}
737	<	else{
738	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	<	}
740	<	info.myAtoms[j]->setType( currentAtom->getType() );
741	<
742	<	#ifdef IS_MPI
743	<
744	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
745	<
746	<	#endif // is_mpi
747	<	}
748	<
749	<	// make the bonds
750	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
612	>	for (j = 0; j < molInfo.nBonds; j++){
613
614	<	exI = theBonds[i].a;
615	<	exJ = theBonds[i].b;
614	>	//if both atoms are in the same rigid body, just skip it
615	>	currentBond = comp_stamps[stampID]->getBond(j);
616	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617
618	<	// exclude_I must always be the smaller of the pair
619	<	if( exI > exJ ){
620	<	tempEx = exI;
621	<	exI = exJ;
622	<	exJ = tempEx;
764	<	}
765	<	#ifdef IS_MPI
766	<
767	<	the_excludes[index*2] =
768	<	the_atoms[exI]->getGlobalIndex() + 1;
769	<	the_excludes[index*2 + 1] =
770	<	the_atoms[exJ]->getGlobalIndex() + 1;
771	<
772	<	#else  // isn't MPI
773	<
774	<	the_excludes[index*2] =     exI + 1;
775	<	the_excludes[index*2 + 1] = exJ + 1;
776	<	// fortran index from 1 (hence the +1 in the indexing)
618	>	tempI = currentBond->getA() + atomOffset;
619	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621	>	else
622	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
623
624	<	#endif  //is_mpi
625	<
626	<	}
624	>	tempJ =  currentBond->getB() + atomOffset;
625	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627	>	else
628	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
629
630	+	consPair = new DistanceConstraintPair(consElement1, consElement2);
631	+	molInfo.myConstraintPairs.push_back(consPair);
632	+	}
633	+	}
634	+
635	+	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636	+	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637	+	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638	+
639	+	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640
641	+	for(size_t m = 0; m < jointAtoms.size(); m++){
642	+	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643	+	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644
645	+	consPair = new JointConstraintPair(consElement1, consElement2);
646	+	molInfo.myConstraintPairs.push_back(consPair);
647	+	}
648
649	<
786	<
787	<
788	<
789	<
790	<
791	<
792	<
793	<
794	<
795	<
796	<	void SimSetup::makeAtoms( void ){
797	<
798	<	int i, j, k, index;
799	<	double ux, uy, uz, uSqr, u;
800	<	AtomStamp* current_atom;
801	<
802	<	DirectionalAtom* dAtom;
803	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
804	<
805	<	lMolIndex = 0;
806	<	molIndex = 0;
807	<	index = 0;
808	<	for( i=0; i<n_components; i++ ){
809	<
810	<	for( j=0; j<components_nmol[i]; j++ ){
811	<
812	<	#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
816	<
817	<	molStart = index;
818	<	nMemb = comp_stamps[i]->getNAtoms();
819	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
820	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
859	<
860	<	#ifdef IS_MPI
649	>	}
650		}
862	–	#endif //is_mpi
651
652	<	molIndex++;
652	>	*/
653	>	// send the arrays off to the forceField for init.
654	>
655	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
656	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
657	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
658	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
659	>	theTorsions);
660	>
661	>	info[k].molecules[i].initialize(molInfo);
662	>
663	>
664	>	atomOffset += molInfo.nAtoms;
665	>	delete[] theBonds;
666	>	delete[] theBends;
667	>	delete[] theTorsions;
668		}
866	–	}
669
868	–	#ifdef IS_MPI
869	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
870	–
871	–	delete[] globalIndex;
670
873	–	mpiSim->mpiRefresh();
874	–	#endif //IS_MPI
875	–
876	–	the_ff->initializeAtoms();
877	–	}
671
672	<	void SimSetup::makeBonds( void ){
672	>	#ifdef IS_MPI
673	>	// Since the globalGroupMembership has been zero filled and we've only
674	>	// poked values into the atoms we know, we can do an Allreduce
675	>	// to get the full globalGroupMembership array (We think).
676	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677	>	// docs said we could.
678
679	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882	<	bond_pair* the_bonds;
883	<	BondStamp* current_bond;
679	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
680
681	<	the_bonds = new bond_pair[tot_bonds];
682	<	index = 0;
683	<	offset = 0;
684	<	molIndex = 0;
681	>	MPI_Allreduce(info[k].globalGroupMembership,
682	>	ggMjunk,
683	>	mpiSim->getNAtomsGlobal(),
684	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685
686	<	for( i=0; i<n_components; i++ ){
687	<
892	<	for( j=0; j<components_nmol[i]; j++ ){
893	<
894	<	#ifdef IS_MPI
895	<	if( mpiSim->getMyMolStart() <= molIndex &&
896	<	molIndex <= mpiSim->getMyMolEnd() ){
897	<	#endif // is_mpi
898	<
899	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
904	<
905	<	exI = the_bonds[index].a;
906	<	exJ = the_bonds[index].b;
907	<
908	<	// exclude_I must always be the smaller of the pair
909	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
914	<
915	<
916	<	#ifdef IS_MPI
917	<
918	<	the_excludes[index*2] =
919	<	the_atoms[exI]->getGlobalIndex() + 1;
920	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
922	<
923	<	#else  // isn't MPI
924	<
925	<	the_excludes[index*2] =     exI + 1;
926	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
936	<	}
937	<	#endif //is_mpi
938	<
939	<	molIndex++;
940	<	}
941	<	}
686	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687	>	info[k].globalGroupMembership[i] = ggMjunk[i];
688
689	<	the_ff->initializeBonds( the_bonds );
690	<	}
689	>	delete[] ggMjunk;
690	>
691	>	#endif
692
946	–	void SimSetup::makeBends( void ){
693
948	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	–	bend_set* the_bends;
950	–	BendStamp* current_bend;
951	–	LinkedAssign* extras;
952	–	LinkedAssign* current_extra;
953	–
694
955	–	the_bends = new bend_set[tot_bends];
956	–	index = 0;
957	–	offset = 0;
958	–	molIndex = 0;
959	–	for( i=0; i<n_components; i++ ){
960	–
961	–	for( j=0; j<components_nmol[i]; j++ ){
962	–
963	–	#ifdef IS_MPI
964	–	if( mpiSim->getMyMolStart() <= molIndex &&
965	–	molIndex <= mpiSim->getMyMolEnd() ){
966	–	#endif // is_mpi
967	–
968	–	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
969	–
970	–	current_bend = comp_stamps[i]->getBend( k );
971	–	the_bends[index].a = current_bend->getA() + offset;
972	–	the_bends[index].b = current_bend->getB() + offset;
973	–	the_bends[index].c = current_bend->getC() + offset;
974	–
975	–	if( current_bend->haveExtras() ){
976	–
977	–	extras = current_bend->getExtras();
978	–	current_extra = extras;
979	–
980	–	while( current_extra != NULL ){
981	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	–
983	–	switch( current_extra->getType() ){
984	–
985	–	case 0:
986	–	the_bends[index].ghost =
987	–	current_extra->getInt() + offset;
988	–	the_bends[index].isGhost = 1;
989	–	break;
990	–
991	–	case 1:
992	–	the_bends[index].ghost =
993	–	(int)current_extra->getDouble() + offset;
994	–	the_bends[index].isGhost = 1;
995	–	break;
996	–
997	–	default:
998	–	sprintf( painCave.errMsg,
999	–	"SimSetup Error: ghostVectorSource was neiter a "
1000	–	"double nor an int.\n"
1001	–	"-->Bend[%d] in %s\n",
1002	–	k, comp_stamps[i]->getID() );
1003	–	painCave.isFatal = 1;
1004	–	simError();
1005	–	}
1006	–	}
1007	–
1008	–	else{
1009	–
1010	–	sprintf( painCave.errMsg,
1011	–	"SimSetup Error: unhandled bend assignment:\n"
1012	–	"    -->%s in Bend[%d] in %s\n",
1013	–	current_extra->getlhs(),
1014	–	k, comp_stamps[i]->getID() );
1015	–	painCave.isFatal = 1;
1016	–	simError();
1017	–	}
1018	–
1019	–	current_extra = current_extra->getNext();
1020	–	}
1021	–	}
1022	–
1023	–	if( !the_bends[index].isGhost ){
1024	–
1025	–	exI = the_bends[index].a;
1026	–	exJ = the_bends[index].c;
1027	–	}
1028	–	else{
1029	–
1030	–	exI = the_bends[index].a;
1031	–	exJ = the_bends[index].b;
1032	–	}
1033	–
1034	–	// exclude_I must always be the smaller of the pair
1035	–	if( exI > exJ ){
1036	–	tempEx = exI;
1037	–	exI = exJ;
1038	–	exJ = tempEx;
1039	–	}
1040	–
1041	–
1042	–	#ifdef IS_MPI
1043	–
1044	–	the_excludes[(index + tot_bonds)*2] =
1045	–	the_atoms[exI]->getGlobalIndex() + 1;
1046	–	the_excludes[(index + tot_bonds)*2 + 1] =
1047	–	the_atoms[exJ]->getGlobalIndex() + 1;
1048	–
1049	–	#else  // isn't MPI
1050	–
1051	–	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	–	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	–	// fortran index from 1 (hence the +1 in the indexing)
1054	–	#endif  //is_mpi
1055	–
1056	–
1057	–	// increment the index and repeat;
1058	–	index++;
1059	–	}
1060	–	offset += comp_stamps[i]->getNAtoms();
1061	–
1062	–	#ifdef IS_MPI
1063	–	}
1064	–	#endif //is_mpi
1065	–
1066	–	molIndex++;
1067	–	}
695		}
696
697		#ifdef IS_MPI
698	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
698	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
699		MPIcheckPoint();
700		#endif // is_mpi
1075	–
701
1077	–	the_ff->initializeBends( the_bends );
702		}
703
704	<	void SimSetup::makeTorsions( void ){
1081	<
1082	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
1085	<
1086	<	the_torsions = new torsion_set[tot_torsions];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1091	<
1092	<	for( j=0; j<components_nmol[i]; j++ ){
1093	<
1094	<	#ifdef IS_MPI
1095	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1098	<
1099	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1100	<
1101	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1106	<
1107	<	exI = the_torsions[index].a;
1108	<	exJ = the_torsions[index].d;
1109	<
1110	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1117	<
1118	<
1119	<	#ifdef IS_MPI
1120	<
1121	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1122	<	the_atoms[exI]->getGlobalIndex() + 1;
1123	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124	<	the_atoms[exJ]->getGlobalIndex() + 1;
1125	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1133	<
1134	<	// increment the index and repeat;
1135	<	index++;
1136	<	}
1137	<	offset += comp_stamps[i]->getNAtoms();
1138	<
1139	<	#ifdef IS_MPI
1140	<	}
1141	<	#endif //is_mpi
1142	<
1143	<	molIndex++;
1144	<	}
1145	<	}
1146	<
1147	<	the_ff->initializeTorsions( the_torsions );
1148	<	}
1149	<
1150	<	void SimSetup::initFromBass( void ){
1151	<
704	>	void SimSetup::initFromBass(void){
705		int i, j, k;
706		int n_cells;
707		double cellx, celly, cellz;
#	Line 1157 | Line 710 | void SimSetup::initFromBass( void ){
710		int n_extra;
711		int have_extra, done;
712
713	<	temp1 = (double)tot_nmol / 4.0;
714	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
715	<	temp3 = ceil( temp2 );
713	>	double vel[3];
714	>	vel[0] = 0.0;
715	>	vel[1] = 0.0;
716	>	vel[2] = 0.0;
717
718	<	have_extra =0;
719	<	if( temp2 < temp3 ){ // we have a non-complete lattice
720	<	have_extra =1;
718	>	temp1 = (double) tot_nmol / 4.0;
719	>	temp2 = pow(temp1, (1.0 / 3.0));
720	>	temp3 = ceil(temp2);
721
722	<	n_cells = (int)temp3 - 1;
723	<	cellx = simnfo->box_x / temp3;
724	<	celly = simnfo->box_y / temp3;
725	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
722	>	have_extra = 0;
723	>	if (temp2 < temp3){
724	>	// we have a non-complete lattice
725	>	have_extra = 1;
726
727	<	if( n_per_extra > 4){
728	<	sprintf( painCave.errMsg,
729	<	"SimSetup error. There has been an error in constructing"
730	<	" the non-complete lattice.\n" );
727	>	n_cells = (int) temp3 - 1;
728	>	cellx = info[0].boxL[0] / temp3;
729	>	celly = info[0].boxL[1] / temp3;
730	>	cellz = info[0].boxL[2] / temp3;
731	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
732	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
733	>	n_per_extra = (int) ceil(temp1);
734	>
735	>	if (n_per_extra > 4){
736	>	sprintf(painCave.errMsg,
737	>	"SimSetup error. There has been an error in constructing"
738	>	" the non-complete lattice.\n");
739		painCave.isFatal = 1;
740		simError();
741		}
742		}
743		else{
744	<	n_cells = (int)temp3;
745	<	cellx = simnfo->box_x / temp3;
746	<	celly = simnfo->box_y / temp3;
747	<	cellz = simnfo->box_z / temp3;
744	>	n_cells = (int) temp3;
745	>	cellx = info[0].boxL[0] / temp3;
746	>	celly = info[0].boxL[1] / temp3;
747	>	cellz = info[0].boxL[2] / temp3;
748		}
749
750		current_mol = 0;
#	Line 1193 | Line 752 | void SimSetup::initFromBass( void ){
752		current_comp = 0;
753		current_atom_ndx = 0;
754
755	<	for( i=0; i < n_cells ; i++ ){
756	<	for( j=0; j < n_cells; j++ ){
757	<	for( k=0; k < n_cells; k++ ){
755	>	for (i = 0; i < n_cells ; i++){
756	>	for (j = 0; j < n_cells; j++){
757	>	for (k = 0; k < n_cells; k++){
758	>	makeElement(i * cellx, j * celly, k * cellz);
759
760	<	makeElement( i * cellx,
1201	<	j * celly,
1202	<	k * cellz );
760	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
761
762	<	makeElement( i * cellx + 0.5 * cellx,
1205	<	j * celly + 0.5 * celly,
1206	<	k * cellz );
762	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
763
764	<	makeElement( i * cellx,
1209	<	j * celly + 0.5 * celly,
1210	<	k * cellz + 0.5 * cellz );
1211	<
1212	<	makeElement( i * cellx + 0.5 * cellx,
1213	<	j * celly,
1214	<	k * cellz + 0.5 * cellz );
764	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
765		}
766		}
767		}
768
769	<	if( have_extra ){
769	>	if (have_extra){
770		done = 0;
771
772		int start_ndx;
773	<	for( i=0; i < (n_cells+1) && !done; i++ ){
774	<	for( j=0; j < (n_cells+1) && !done; j++ ){
773	>	for (i = 0; i < (n_cells + 1) && !done; i++){
774	>	for (j = 0; j < (n_cells + 1) && !done; j++){
775	>	if (i < n_cells){
776	>	if (j < n_cells){
777	>	start_ndx = n_cells;
778	>	}
779	>	else
780	>	start_ndx = 0;
781	>	}
782	>	else
783	>	start_ndx = 0;
784
785	<	if( i < n_cells ){
785	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
786	>	makeElement(i * cellx, j * celly, k * cellz);
787	>	done = (current_mol >= tot_nmol);
788
789	<	if( j < n_cells ){
790	<	start_ndx = n_cells;
791	<	}
792	<	else start_ndx = 0;
793	<	}
1233	<	else start_ndx = 0;
789	>	if (!done && n_per_extra > 1){
790	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
791	>	k * cellz);
792	>	done = (current_mol >= tot_nmol);
793	>	}
794
795	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
795	>	if (!done && n_per_extra > 2){
796	>	makeElement(i * cellx, j * celly + 0.5 * celly,
797	>	k * cellz + 0.5 * cellz);
798	>	done = (current_mol >= tot_nmol);
799	>	}
800
801	<	makeElement( i * cellx,
802	<	j * celly,
803	<	k * cellz );
804	<	done = ( current_mol >= tot_nmol );
805	<
806	<	if( !done && n_per_extra > 1 ){
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1248	<
1249	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1255	<
1256	<	if( !done && n_per_extra > 3){
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly,
1259	<	k * cellz + 0.5 * cellz );
1260	<	done = ( current_mol >= tot_nmol );
1261	<	}
1262	<	}
801	>	if (!done && n_per_extra > 3){
802	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
803	>	k * cellz + 0.5 * cellz);
804	>	done = (current_mol >= tot_nmol);
805	>	}
806	>	}
807		}
808		}
809		}
810
811	<
812	<	for( i=0; i<simnfo->n_atoms; i++ ){
1269	<	simnfo->atoms[i]->set_vx( 0.0 );
1270	<	simnfo->atoms[i]->set_vy( 0.0 );
1271	<	simnfo->atoms[i]->set_vz( 0.0 );
811	>	for (i = 0; i < info[0].n_atoms; i++){
812	>	info[0].atoms[i]->setVel(vel);
813		}
814		}
815
816	<	void SimSetup::makeElement( double x, double y, double z ){
1276	<
816	>	void SimSetup::makeElement(double x, double y, double z){
817		int k;
818		AtomStamp* current_atom;
819		DirectionalAtom* dAtom;
820		double rotMat[3][3];
821	+	double pos[3];
822
823	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
824	<
825	<	current_atom = comp_stamps[current_comp]->getAtom( k );
826	<	if( !current_atom->havePosition() ){
827	<	sprintf( painCave.errMsg,
828	<	"SimSetup:initFromBass error.\n"
829	<	"\tComponent %s, atom %s does not have a position specified.\n"
830	<	"\tThe initialization routine is unable to give a start"
831	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
823	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
824	>	current_atom = comp_stamps[current_comp]->getAtom(k);
825	>	if (!current_atom->havePosition()){
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup:initFromBass error.\n"
828	>	"\tComponent %s, atom %s does not have a position specified.\n"
829	>	"\tThe initialization routine is unable to give a start"
830	>	" position.\n",
831	>	comp_stamps[current_comp]->getID(), current_atom->getType());
832		painCave.isFatal = 1;
833		simError();
834		}
835
836	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
837	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
838	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
836	>	pos[0] = x + current_atom->getPosX();
837	>	pos[1] = y + current_atom->getPosY();
838	>	pos[2] = z + current_atom->getPosZ();
839
840	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
840	>	info[0].atoms[current_atom_ndx]->setPos(pos);
841
842	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
842	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
843	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
844
845		rotMat[0][0] = 1.0;
846		rotMat[0][1] = 0.0;
#	Line 1313 | Line 853 | void SimSetup::makeElement( double x, double y, double
853		rotMat[2][0] = 0.0;
854		rotMat[2][1] = 0.0;
855		rotMat[2][2] = 1.0;
856	+
857	+	dAtom->setA(rotMat);
858	+	}
859	+
860	+	current_atom_ndx++;
861	+	}
862	+
863	+	current_mol++;
864	+	current_comp_mol++;
865	+
866	+	if (current_comp_mol >= components_nmol[current_comp]){
867	+	current_comp_mol = 0;
868	+	current_comp++;
869	+	}
870	+	}
871	+
872	+
873	+	void SimSetup::gatherInfo(void){
874	+	int i;
875	+
876	+	ensembleCase = -1;
877	+	ffCase = -1;
878	+
879	+	// set the easy ones first
880	+
881	+	for (i = 0; i < nInfo; i++){
882	+	info[i].target_temp = globals->getTargetTemp();
883	+	info[i].dt = globals->getDt();
884	+	info[i].run_time = globals->getRunTime();
885	+	}
886	+	n_components = globals->getNComponents();
887	+
888	+
889	+	// get the forceField
890	+
891	+	strcpy(force_field, globals->getForceField());
892	+
893	+	if (!strcasecmp(force_field, "DUFF")){
894	+	ffCase = FF_DUFF;
895	+	}
896	+	else if (!strcasecmp(force_field, "LJ")){
897	+	ffCase = FF_LJ;
898	+	}
899	+	else if (!strcasecmp(force_field, "EAM")){
900	+	ffCase = FF_EAM;
901	+	}
902	+	else if (!strcasecmp(force_field, "WATER")){
903	+	ffCase = FF_H2O;
904	+	}
905	+	else{
906	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
907	+	force_field);
908	+	painCave.isFatal = 1;
909	+	simError();
910	+	}
911	+
912	+	// get the ensemble
913	+
914	+	strcpy(ensemble, globals->getEnsemble());
915	+
916	+	if (!strcasecmp(ensemble, "NVE")){
917	+	ensembleCase = NVE_ENS;
918	+	}
919	+	else if (!strcasecmp(ensemble, "NVT")){
920	+	ensembleCase = NVT_ENS;
921	+	}
922	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
923	+	ensembleCase = NPTi_ENS;
924	+	}
925	+	else if (!strcasecmp(ensemble, "NPTf")){
926	+	ensembleCase = NPTf_ENS;
927	+	}
928	+	else if (!strcasecmp(ensemble, "NPTxyz")){
929	+	ensembleCase = NPTxyz_ENS;
930	+	}
931	+	else{
932	+	sprintf(painCave.errMsg,
933	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
934	+	"\treverting to NVE for this simulation.\n",
935	+	ensemble);
936	+	painCave.isFatal = 0;
937	+	simError();
938	+	strcpy(ensemble, "NVE");
939	+	ensembleCase = NVE_ENS;
940	+	}
941	+
942	+	for (i = 0; i < nInfo; i++){
943	+	strcpy(info[i].ensemble, ensemble);
944	+
945	+	// get the mixing rule
946	+
947	+	strcpy(info[i].mixingRule, globals->getMixingRule());
948	+	info[i].usePBC = globals->getPBC();
949	+	}
950	+
951	+	// get the components and calculate the tot_nMol and indvidual n_mol
952	+
953	+	the_components = globals->getComponents();
954	+	components_nmol = new int[n_components];
955	+
956	+
957	+	if (!globals->haveNMol()){
958	+	// we don't have the total number of molecules, so we assume it is
959	+	// given in each component
960	+
961	+	tot_nmol = 0;
962	+	for (i = 0; i < n_components; i++){
963	+	if (!the_components[i]->haveNMol()){
964	+	// we have a problem
965	+	sprintf(painCave.errMsg,
966	+	"SimSetup Error. No global NMol or component NMol given.\n"
967	+	"\tCannot calculate the number of atoms.\n");
968	+	painCave.isFatal = 1;
969	+	simError();
970	+	}
971	+
972	+	tot_nmol += the_components[i]->getNMol();
973	+	components_nmol[i] = the_components[i]->getNMol();
974	+	}
975	+	}
976	+	else{
977	+	sprintf(painCave.errMsg,
978	+	"SimSetup error.\n"
979	+	"\tSorry, the ability to specify total"
980	+	" nMols and then give molfractions in the components\n"
981	+	"\tis not currently supported."
982	+	" Please give nMol in the components.\n");
983	+	painCave.isFatal = 1;
984	+	simError();
985	+	}
986	+
987	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
988	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
989	+	sprintf(painCave.errMsg,
990	+	"Sample time is not divisible by dt.\n"
991	+	"\tThis will result in samples that are not uniformly\n"
992	+	"\tdistributed in time.  If this is a problem, change\n"
993	+	"\tyour sampleTime variable.\n");
994	+	painCave.isFatal = 0;
995	+	simError();
996	+	}
997	+
998	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
999	+	sprintf(painCave.errMsg,
1000	+	"Status time is not divisible by dt.\n"
1001	+	"\tThis will result in status reports that are not uniformly\n"
1002	+	"\tdistributed in time.  If this is a problem, change \n"
1003	+	"\tyour statusTime variable.\n");
1004	+	painCave.isFatal = 0;
1005	+	simError();
1006	+	}
1007	+
1008	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1009	+	sprintf(painCave.errMsg,
1010	+	"Thermal time is not divisible by dt.\n"
1011	+	"\tThis will result in thermalizations that are not uniformly\n"
1012	+	"\tdistributed in time.  If this is a problem, change \n"
1013	+	"\tyour thermalTime variable.\n");
1014	+	painCave.isFatal = 0;
1015	+	simError();
1016	+	}
1017	+
1018	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1019	+	sprintf(painCave.errMsg,
1020	+	"Reset time is not divisible by dt.\n"
1021	+	"\tThis will result in integrator resets that are not uniformly\n"
1022	+	"\tdistributed in time.  If this is a problem, change\n"
1023	+	"\tyour resetTime variable.\n");
1024	+	painCave.isFatal = 0;
1025	+	simError();
1026	+	}
1027	+
1028	+	// set the status, sample, and thermal kick times
1029	+
1030	+	for (i = 0; i < nInfo; i++){
1031	+	if (globals->haveSampleTime()){
1032	+	info[i].sampleTime = globals->getSampleTime();
1033	+	info[i].statusTime = info[i].sampleTime;
1034	+	}
1035	+	else{
1036	+	info[i].sampleTime = globals->getRunTime();
1037	+	info[i].statusTime = info[i].sampleTime;
1038	+	}
1039	+
1040	+	if (globals->haveStatusTime()){
1041	+	info[i].statusTime = globals->getStatusTime();
1042	+	}
1043	+
1044	+	if (globals->haveThermalTime()){
1045	+	info[i].thermalTime = globals->getThermalTime();
1046	+	} else {
1047	+	info[i].thermalTime = globals->getRunTime();
1048	+	}
1049	+
1050	+	info[i].resetIntegrator = 0;
1051	+	if( globals->haveResetTime() ){
1052	+	info[i].resetTime = globals->getResetTime();
1053	+	info[i].resetIntegrator = 1;
1054	+	}
1055	+
1056	+	// check for the temperature set flag
1057	+
1058	+	if (globals->haveTempSet())
1059	+	info[i].setTemp = globals->getTempSet();
1060	+
1061	+	// check for the extended State init
1062	+
1063	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1064	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065	+
1066	+	// check for thermodynamic integration
1067	+	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069	+	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070	+	info[i].thermIntLambda = globals->getThermIntLambda();
1071	+	info[i].thermIntK = globals->getThermIntK();
1072	+
1073	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1074	+	info[i].restraint = myRestraint;
1075	+	}
1076	+	else {
1077	+	sprintf(painCave.errMsg,
1078	+	"SimSetup Error:\n"
1079	+	"\tKeyword useSolidThermInt was set to 'true' but\n"
1080	+	"\tthermodynamicIntegrationLambda (and/or\n"
1081	+	"\tthermodynamicIntegrationK) was not specified.\n"
1082	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1083	+	painCave.isFatal = 1;
1084	+	simError();
1085	+	}
1086	+	}
1087	+	else if(globals->getUseLiquidThermInt()) {
1088	+	if (globals->getUseSolidThermInt()) {
1089	+	sprintf( painCave.errMsg,
1090	+	"SimSetup Warning: It appears that you have both solid and\n"
1091	+	"\tliquid thermodynamic integration activated in your .bass\n"
1092	+	"\tfile. To avoid confusion, specify only one technique in\n"
1093	+	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1094	+	"\twill be assumed for the current simulation. If this is not\n"
1095	+	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1096	+	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097	+	painCave.isFatal = 0;
1098	+	simError();
1099	+	}
1100	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101	+	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102	+	info[i].thermIntLambda = globals->getThermIntLambda();
1103	+	info[i].thermIntK = globals->getThermIntK();
1104	+	}
1105	+	else {
1106	+	sprintf(painCave.errMsg,
1107	+	"SimSetup Error:\n"
1108	+	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1109	+	"\tthermodynamicIntegrationLambda (and/or\n"
1110	+	"\tthermodynamicIntegrationK) was not specified.\n"
1111	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
1112	+	painCave.isFatal = 1;
1113	+	simError();
1114	+	}
1115	+	}
1116	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1117	+	sprintf(painCave.errMsg,
1118	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1119	+	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120	+	"\t'true' in your .bass file.  These keywords are set to\n"
1121	+	"\t'false' by default, so your lambda and/or k values are\n"
1122	+	"\tbeing ignored.\n");
1123	+	painCave.isFatal = 0;
1124	+	simError();
1125	+	}
1126	+	}
1127	+
1128	+	//setup seed for random number generator
1129	+	int seedValue;
1130	+
1131	+	if (globals->haveSeed()){
1132	+	seedValue = globals->getSeed();
1133	+
1134	+	if(seedValue / 1E9 == 0){
1135	+	sprintf(painCave.errMsg,
1136	+	"Seed for sprng library should contain at least 9 digits\n"
1137	+	"OOPSE will generate a seed for user\n");
1138	+	painCave.isFatal = 0;
1139	+	simError();
1140	+
1141	+	//using seed generated by system instead of invalid seed set by user
1142	+	#ifndef IS_MPI
1143	+	seedValue = make_sprng_seed();
1144	+	#else
1145	+	if (worldRank == 0){
1146	+	seedValue = make_sprng_seed();
1147	+	}
1148	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1149	+	#endif
1150	+	}
1151	+	}//end of if branch of globals->haveSeed()
1152	+	else{
1153	+
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}//end of globals->haveSeed()
1163	+
1164	+	for (int i = 0; i < nInfo; i++){
1165	+	info[i].setSeed(seedValue);
1166	+	}
1167	+
1168	+	#ifdef IS_MPI
1169	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1170	+	MPIcheckPoint();
1171	+	#endif // is_mpi
1172	+	}
1173	+
1174	+
1175	+	void SimSetup::finalInfoCheck(void){
1176	+	int index;
1177	+	int usesDipoles;
1178	+	int usesCharges;
1179	+	int i;
1180	+
1181	+	for (i = 0; i < nInfo; i++){
1182	+	// check electrostatic parameters
1183	+
1184	+	index = 0;
1185	+	usesDipoles = 0;
1186	+	while ((index < info[i].n_atoms) && !usesDipoles){
1187	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1188	+	index++;
1189	+	}
1190	+	index = 0;
1191	+	usesCharges = 0;
1192	+	while ((index < info[i].n_atoms) && !usesCharges){
1193	+	usesCharges= (info[i].atoms[index])->hasCharge();
1194	+	index++;
1195	+	}
1196	+	#ifdef IS_MPI
1197	+	int myUse = usesDipoles;
1198	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1199	+	#endif //is_mpi
1200	+
1201	+	double theRcut, theRsw;
1202	+
1203	+	if (globals->haveRcut()) {
1204	+	theRcut = globals->getRcut();
1205	+
1206	+	if (globals->haveRsw())
1207	+	theRsw = globals->getRsw();
1208	+	else
1209	+	theRsw = theRcut;
1210	+
1211	+	info[i].setDefaultRcut(theRcut, theRsw);
1212	+
1213	+	} else {
1214	+
1215	+	the_ff->calcRcut();
1216	+	theRcut = info[i].getRcut();
1217	+
1218	+	if (globals->haveRsw())
1219	+	theRsw = globals->getRsw();
1220	+	else
1221	+	theRsw = theRcut;
1222	+
1223	+	info[i].setDefaultRcut(theRcut, theRsw);
1224	+	}
1225
1226	<	dAtom->setA( rotMat );
1226	>	if (globals->getUseRF()){
1227	>	info[i].useReactionField = 1;
1228	>
1229	>	if (!globals->haveRcut()){
1230	>	sprintf(painCave.errMsg,
1231	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1232	>	"\tOOPSE will use a default value of 15.0 angstroms"
1233	>	"\tfor the cutoffRadius.\n");
1234	>	painCave.isFatal = 0;
1235	>	simError();
1236	>	theRcut = 15.0;
1237	>	}
1238	>	else{
1239	>	theRcut = globals->getRcut();
1240	>	}
1241	>
1242	>	if (!globals->haveRsw()){
1243	>	sprintf(painCave.errMsg,
1244	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1245	>	"\tOOPSE will use a default value of\n"
1246	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1247	>	painCave.isFatal = 0;
1248	>	simError();
1249	>	theRsw = 0.95 * theRcut;
1250	>	}
1251	>	else{
1252	>	theRsw = globals->getRsw();
1253	>	}
1254	>
1255	>	info[i].setDefaultRcut(theRcut, theRsw);
1256	>
1257	>	if (!globals->haveDielectric()){
1258	>	sprintf(painCave.errMsg,
1259	>	"SimSetup Error: No Dielectric constant was set.\n"
1260	>	"\tYou are trying to use Reaction Field without"
1261	>	"\tsetting a dielectric constant!\n");
1262	>	painCave.isFatal = 1;
1263	>	simError();
1264	>	}
1265	>	info[i].dielectric = globals->getDielectric();
1266		}
1267	+	else{
1268	+	if (usesDipoles || usesCharges){
1269
1270	<	current_atom_ndx++;
1270	>	if (!globals->haveRcut()){
1271	>	sprintf(painCave.errMsg,
1272	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1273	>	"\tOOPSE will use a default value of 15.0 angstroms"
1274	>	"\tfor the cutoffRadius.\n");
1275	>	painCave.isFatal = 0;
1276	>	simError();
1277	>	theRcut = 15.0;
1278	>	}
1279	>	else{
1280	>	theRcut = globals->getRcut();
1281	>	}
1282	>
1283	>	if (!globals->haveRsw()){
1284	>	sprintf(painCave.errMsg,
1285	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1286	>	"\tOOPSE will use a default value of\n"
1287	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1288	>	painCave.isFatal = 0;
1289	>	simError();
1290	>	theRsw = 0.95 * theRcut;
1291	>	}
1292	>	else{
1293	>	theRsw = globals->getRsw();
1294	>	}
1295	>
1296	>	info[i].setDefaultRcut(theRcut, theRsw);
1297	>
1298	>	}
1299	>	}
1300		}
1301	+	#ifdef IS_MPI
1302	+	strcpy(checkPointMsg, "post processing checks out");
1303	+	MPIcheckPoint();
1304	+	#endif // is_mpi
1305
1306	<	current_mol++;
1307	<	current_comp_mol++;
1306	>	// clean up the forcefield
1307	>	the_ff->cleanMe();
1308	>	}
1309	>
1310	>	void SimSetup::initSystemCoords(void){
1311	>	int i;
1312
1313	<	if( current_comp_mol >= components_nmol[current_comp] ){
1313	>	char* inName;
1314
1315	<	current_comp_mol = 0;
1316	<	current_comp++;
1315	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1316	>
1317	>	for (i = 0; i < info[0].n_atoms; i++)
1318	>	info[0].atoms[i]->setCoords();
1319	>
1320	>	if (globals->haveInitialConfig()){
1321	>	InitializeFromFile* fileInit;
1322	>	#ifdef IS_MPI // is_mpi
1323	>	if (worldRank == 0){
1324	>	#endif //is_mpi
1325	>	inName = globals->getInitialConfig();
1326	>	fileInit = new InitializeFromFile(inName);
1327	>	#ifdef IS_MPI
1328	>	}
1329	>	else
1330	>	fileInit = new InitializeFromFile(NULL);
1331	>	#endif
1332	>	fileInit->readInit(info); // default velocities on
1333	>
1334	>	delete fileInit;
1335	>	}
1336	>	else{
1337	>
1338	>	// no init from bass
1339	>
1340	>	sprintf(painCave.errMsg,
1341	>	"Cannot intialize a simulation without an initial configuration file.\n");
1342	>	painCave.isFatal = 1;;
1343	>	simError();
1344	>
1345	>	}
1346	>
1347	>	#ifdef IS_MPI
1348	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1349	>	MPIcheckPoint();
1350	>	#endif // is_mpi
1351	>	}
1352	>
1353	>
1354	>	void SimSetup::makeOutNames(void){
1355	>	int k;
1356	>
1357	>
1358	>	for (k = 0; k < nInfo; k++){
1359	>	#ifdef IS_MPI
1360	>	if (worldRank == 0){
1361	>	#endif // is_mpi
1362	>
1363	>	if (globals->haveFinalConfig()){
1364	>	strcpy(info[k].finalName, globals->getFinalConfig());
1365	>	}
1366	>	else{
1367	>	strcpy(info[k].finalName, inFileName);
1368	>	char* endTest;
1369	>	int nameLength = strlen(info[k].finalName);
1370	>	endTest = &(info[k].finalName[nameLength - 5]);
1371	>	if (!strcmp(endTest, ".bass")){
1372	>	strcpy(endTest, ".eor");
1373	>	}
1374	>	else if (!strcmp(endTest, ".BASS")){
1375	>	strcpy(endTest, ".eor");
1376	>	}
1377	>	else{
1378	>	endTest = &(info[k].finalName[nameLength - 4]);
1379	>	if (!strcmp(endTest, ".bss")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else if (!strcmp(endTest, ".mdl")){
1383	>	strcpy(endTest, ".eor");
1384	>	}
1385	>	else{
1386	>	strcat(info[k].finalName, ".eor");
1387	>	}
1388	>	}
1389	>	}
1390	>
1391	>	// make the sample and status out names
1392	>
1393	>	strcpy(info[k].sampleName, inFileName);
1394	>	char* endTest;
1395	>	int nameLength = strlen(info[k].sampleName);
1396	>	endTest = &(info[k].sampleName[nameLength - 5]);
1397	>	if (!strcmp(endTest, ".bass")){
1398	>	strcpy(endTest, ".dump");
1399	>	}
1400	>	else if (!strcmp(endTest, ".BASS")){
1401	>	strcpy(endTest, ".dump");
1402	>	}
1403	>	else{
1404	>	endTest = &(info[k].sampleName[nameLength - 4]);
1405	>	if (!strcmp(endTest, ".bss")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else if (!strcmp(endTest, ".mdl")){
1409	>	strcpy(endTest, ".dump");
1410	>	}
1411	>	else{
1412	>	strcat(info[k].sampleName, ".dump");
1413	>	}
1414	>	}
1415	>
1416	>	strcpy(info[k].statusName, inFileName);
1417	>	nameLength = strlen(info[k].statusName);
1418	>	endTest = &(info[k].statusName[nameLength - 5]);
1419	>	if (!strcmp(endTest, ".bass")){
1420	>	strcpy(endTest, ".stat");
1421	>	}
1422	>	else if (!strcmp(endTest, ".BASS")){
1423	>	strcpy(endTest, ".stat");
1424	>	}
1425	>	else{
1426	>	endTest = &(info[k].statusName[nameLength - 4]);
1427	>	if (!strcmp(endTest, ".bss")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else if (!strcmp(endTest, ".mdl")){
1431	>	strcpy(endTest, ".stat");
1432	>	}
1433	>	else{
1434	>	strcat(info[k].statusName, ".stat");
1435	>	}
1436	>	}
1437	>
1438	>	strcpy(info[k].rawPotName, inFileName);
1439	>	nameLength = strlen(info[k].rawPotName);
1440	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1441	>	if (!strcmp(endTest, ".bass")){
1442	>	strcpy(endTest, ".raw");
1443	>	}
1444	>	else if (!strcmp(endTest, ".BASS")){
1445	>	strcpy(endTest, ".raw");
1446	>	}
1447	>	else{
1448	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1449	>	if (!strcmp(endTest, ".bss")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else if (!strcmp(endTest, ".mdl")){
1453	>	strcpy(endTest, ".raw");
1454	>	}
1455	>	else{
1456	>	strcat(info[k].rawPotName, ".raw");
1457	>	}
1458	>	}
1459	>
1460	>	#ifdef IS_MPI
1461	>
1462	>	}
1463	>	#endif // is_mpi
1464	>	}
1465	>	}
1466	>
1467	>
1468	>	void SimSetup::sysObjectsCreation(void){
1469	>	int i, k;
1470	>
1471	>	// create the forceField
1472	>
1473	>	createFF();
1474	>
1475	>	// extract componentList
1476	>
1477	>	compList();
1478	>
1479	>	// calc the number of atoms, bond, bends, and torsions
1480	>
1481	>	calcSysValues();
1482	>
1483	>	#ifdef IS_MPI
1484	>	// divide the molecules among the processors
1485	>
1486	>	mpiMolDivide();
1487	>	#endif //is_mpi
1488	>
1489	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1490	>
1491	>	makeSysArrays();
1492	>
1493	>	// make and initialize the molecules (all but atomic coordinates)
1494	>
1495	>	makeMolecules();
1496	>
1497	>	for (k = 0; k < nInfo; k++){
1498	>	info[k].identArray = new int[info[k].n_atoms];
1499	>	for (i = 0; i < info[k].n_atoms; i++){
1500	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1501	>	}
1502		}
1503		}
1504	+
1505	+
1506	+	void SimSetup::createFF(void){
1507	+	switch (ffCase){
1508	+	case FF_DUFF:
1509	+	the_ff = new DUFF();
1510	+	break;
1511	+
1512	+	case FF_LJ:
1513	+	the_ff = new LJFF();
1514	+	break;
1515	+
1516	+	case FF_EAM:
1517	+	the_ff = new EAM_FF();
1518	+	break;
1519	+
1520	+	case FF_H2O:
1521	+	the_ff = new WATER();
1522	+	break;
1523	+
1524	+	default:
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1527	+	painCave.isFatal = 1;
1528	+	simError();
1529	+	}
1530	+
1531	+	#ifdef IS_MPI
1532	+	strcpy(checkPointMsg, "ForceField creation successful");
1533	+	MPIcheckPoint();
1534	+	#endif // is_mpi
1535	+	}
1536	+
1537	+
1538	+	void SimSetup::compList(void){
1539	+	int i;
1540	+	char* id;
1541	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1542	+	LinkedMolStamp* currentStamp = NULL;
1543	+	comp_stamps = new MoleculeStamp * [n_components];
1544	+	bool haveCutoffGroups;
1545	+
1546	+	haveCutoffGroups = false;
1547	+
1548	+	// make an array of molecule stamps that match the components used.
1549	+	// also extract the used stamps out into a separate linked list
1550	+
1551	+	for (i = 0; i < nInfo; i++){
1552	+	info[i].nComponents = n_components;
1553	+	info[i].componentsNmol = components_nmol;
1554	+	info[i].compStamps = comp_stamps;
1555	+	info[i].headStamp = headStamp;
1556	+	}
1557	+
1558	+
1559	+	for (i = 0; i < n_components; i++){
1560	+	id = the_components[i]->getType();
1561	+	comp_stamps[i] = NULL;
1562	+
1563	+	// check to make sure the component isn't already in the list
1564	+
1565	+	comp_stamps[i] = headStamp->match(id);
1566	+	if (comp_stamps[i] == NULL){
1567	+	// extract the component from the list;
1568	+
1569	+	currentStamp = stamps->extractMolStamp(id);
1570	+	if (currentStamp == NULL){
1571	+	sprintf(painCave.errMsg,
1572	+	"SimSetup error: Component \"%s\" was not found in the "
1573	+	"list of declared molecules\n",
1574	+	id);
1575	+	painCave.isFatal = 1;
1576	+	simError();
1577	+	}
1578	+
1579	+	headStamp->add(currentStamp);
1580	+	comp_stamps[i] = headStamp->match(id);
1581	+	}
1582	+
1583	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1584	+	haveCutoffGroups = true;
1585	+	}
1586	+
1587	+	for (i = 0; i < nInfo; i++)
1588	+	info[i].haveCutoffGroups = haveCutoffGroups;
1589	+
1590	+	#ifdef IS_MPI
1591	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1592	+	MPIcheckPoint();
1593	+	#endif // is_mpi
1594	+	}
1595	+
1596	+	void SimSetup::calcSysValues(void){
1597	+	int i, j;
1598	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1599	+
1600	+	int* molMembershipArray;
1601	+	CutoffGroupStamp* cg;
1602	+
1603	+	tot_atoms = 0;
1604	+	tot_bonds = 0;
1605	+	tot_bends = 0;
1606	+	tot_torsions = 0;
1607	+	tot_rigid = 0;
1608	+	tot_groups = 0;
1609	+	for (i = 0; i < n_components; i++){
1610	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1611	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1612	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1613	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1614	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1615	+
1616	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1617	+	atomsingroups = 0;
1618	+	for (j=0; j < ncutgroups; j++) {
1619	+	cg = comp_stamps[i]->getCutoffGroup(j);
1620	+	atomsingroups += cg->getNMembers();
1621	+	}
1622	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1623	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1624	+	}
1625	+
1626	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1627	+	molMembershipArray = new int[tot_atoms];
1628	+
1629	+	for (i = 0; i < nInfo; i++){
1630	+	info[i].n_atoms = tot_atoms;
1631	+	info[i].n_bonds = tot_bonds;
1632	+	info[i].n_bends = tot_bends;
1633	+	info[i].n_torsions = tot_torsions;
1634	+	info[i].n_SRI = tot_SRI;
1635	+	info[i].n_mol = tot_nmol;
1636	+	info[i].ngroup = tot_groups;
1637	+	info[i].molMembershipArray = molMembershipArray;
1638	+	}
1639	+	}
1640	+
1641	+	#ifdef IS_MPI
1642	+
1643	+	void SimSetup::mpiMolDivide(void){
1644	+	int i, j, k;
1645	+	int localMol, allMol;
1646	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1647	+	int local_rigid, local_groups;
1648	+	vector<int> globalMolIndex;
1649	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1650	+	CutoffGroupStamp* cg;
1651	+
1652	+	mpiSim = new mpiSimulation(info);
1653	+
1654	+	mpiSim->divideLabor();
1655	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656	+	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1658	+
1659	+	// set up the local variables
1660	+
1661	+	mol2proc = mpiSim->getMolToProcMap();
1662	+	molCompType = mpiSim->getMolComponentType();
1663	+
1664	+	allMol = 0;
1665	+	localMol = 0;
1666	+	local_atoms = 0;
1667	+	local_bonds = 0;
1668	+	local_bends = 0;
1669	+	local_torsions = 0;
1670	+	local_rigid = 0;
1671	+	local_groups = 0;
1672	+	globalAtomCounter = 0;
1673	+
1674	+	for (i = 0; i < n_components; i++){
1675	+	for (j = 0; j < components_nmol[i]; j++){
1676	+	if (mol2proc[allMol] == worldRank){
1677	+	local_atoms += comp_stamps[i]->getNAtoms();
1678	+	local_bonds += comp_stamps[i]->getNBonds();
1679	+	local_bends += comp_stamps[i]->getNBends();
1680	+	local_torsions += comp_stamps[i]->getNTorsions();
1681	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1682	+
1683	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1684	+	atomsingroups = 0;
1685	+	for (k=0; k < ncutgroups; k++) {
1686	+	cg = comp_stamps[i]->getCutoffGroup(k);
1687	+	atomsingroups += cg->getNMembers();
1688	+	}
1689	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1690	+	ncutgroups;
1691	+	local_groups += ngroupsinstamp;
1692	+
1693	+	localMol++;
1694	+	}
1695	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1696	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1697	+	globalAtomCounter++;
1698	+	}
1699	+
1700	+	allMol++;
1701	+	}
1702	+	}
1703	+	local_SRI = local_bonds + local_bends + local_torsions;
1704	+
1705	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1706	+
1707	+	if (local_atoms != info[0].n_atoms){
1708	+	sprintf(painCave.errMsg,
1709	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1710	+	"\tlocalAtom (%d) are not equal.\n",
1711	+	info[0].n_atoms, local_atoms);
1712	+	painCave.isFatal = 1;
1713	+	simError();
1714	+	}
1715	+
1716	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1717	+	if (local_groups != info[0].ngroup){
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1720	+	"\tlocalGroups (%d) are not equal.\n",
1721	+	info[0].ngroup, local_groups);
1722	+	painCave.isFatal = 1;
1723	+	simError();
1724	+	}
1725	+
1726	+	info[0].n_bonds = local_bonds;
1727	+	info[0].n_bends = local_bends;
1728	+	info[0].n_torsions = local_torsions;
1729	+	info[0].n_SRI = local_SRI;
1730	+	info[0].n_mol = localMol;
1731	+
1732	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1733	+	MPIcheckPoint();
1734	+	}
1735	+
1736	+	#endif // is_mpi
1737	+
1738	+
1739	+	void SimSetup::makeSysArrays(void){
1740	+
1741	+	#ifndef IS_MPI
1742	+	int k, j;
1743	+	#endif // is_mpi
1744	+	int i, l;
1745	+
1746	+	Atom** the_atoms;
1747	+	Molecule* the_molecules;
1748	+
1749	+	for (l = 0; l < nInfo; l++){
1750	+	// create the atom and short range interaction arrays
1751	+
1752	+	the_atoms = new Atom * [info[l].n_atoms];
1753	+	the_molecules = new Molecule[info[l].n_mol];
1754	+	int molIndex;
1755	+
1756	+	// initialize the molecule's stampID's
1757	+
1758	+	#ifdef IS_MPI
1759	+
1760	+
1761	+	molIndex = 0;
1762	+	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1763	+	if (mol2proc[i] == worldRank){
1764	+	the_molecules[molIndex].setStampID(molCompType[i]);
1765	+	the_molecules[molIndex].setMyIndex(molIndex);
1766	+	the_molecules[molIndex].setGlobalIndex(i);
1767	+	molIndex++;
1768	+	}
1769	+	}
1770	+
1771	+	#else // is_mpi
1772	+
1773	+	molIndex = 0;
1774	+	globalAtomCounter = 0;
1775	+	for (i = 0; i < n_components; i++){
1776	+	for (j = 0; j < components_nmol[i]; j++){
1777	+	the_molecules[molIndex].setStampID(i);
1778	+	the_molecules[molIndex].setMyIndex(molIndex);
1779	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1780	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1781	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1782	+	globalAtomCounter++;
1783	+	}
1784	+	molIndex++;
1785	+	}
1786	+	}
1787	+
1788	+
1789	+	#endif // is_mpi
1790	+
1791	+	info[l].globalExcludes = new int;
1792	+	info[l].globalExcludes[0] = 0;
1793	+
1794	+	// set the arrays into the SimInfo object
1795	+
1796	+	info[l].atoms = the_atoms;
1797	+	info[l].molecules = the_molecules;
1798	+	info[l].nGlobalExcludes = 0;
1799	+
1800	+	the_ff->setSimInfo(info);
1801	+	}
1802	+	}
1803	+
1804	+	void SimSetup::makeIntegrator(void){
1805	+	int k;
1806	+
1807	+	NVE<RealIntegrator>* myNVE = NULL;
1808	+	NVT<RealIntegrator>* myNVT = NULL;
1809	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1810	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1811	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1812	+
1813	+	for (k = 0; k < nInfo; k++){
1814	+	switch (ensembleCase){
1815	+	case NVE_ENS:
1816	+	if (globals->haveZconstraints()){
1817	+	setupZConstraint(info[k]);
1818	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1819	+	}
1820	+	else{
1821	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1822	+	}
1823	+
1824	+	info->the_integrator = myNVE;
1825	+	break;
1826	+
1827	+	case NVT_ENS:
1828	+	if (globals->haveZconstraints()){
1829	+	setupZConstraint(info[k]);
1830	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1831	+	}
1832	+	else
1833	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1834	+
1835	+	myNVT->setTargetTemp(globals->getTargetTemp());
1836	+
1837	+	if (globals->haveTauThermostat())
1838	+	myNVT->setTauThermostat(globals->getTauThermostat());
1839	+	else{
1840	+	sprintf(painCave.errMsg,
1841	+	"SimSetup error: If you use the NVT\n"
1842	+	"\tensemble, you must set tauThermostat.\n");
1843	+	painCave.isFatal = 1;
1844	+	simError();
1845	+	}
1846	+
1847	+	info->the_integrator = myNVT;
1848	+	break;
1849	+
1850	+	case NPTi_ENS:
1851	+	if (globals->haveZconstraints()){
1852	+	setupZConstraint(info[k]);
1853	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1854	+	}
1855	+	else
1856	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1857	+
1858	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1859	+
1860	+	if (globals->haveTargetPressure())
1861	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1862	+	else{
1863	+	sprintf(painCave.errMsg,
1864	+	"SimSetup error: If you use a constant pressure\n"
1865	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1866	+	painCave.isFatal = 1;
1867	+	simError();
1868	+	}
1869	+
1870	+	if (globals->haveTauThermostat())
1871	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1872	+	else{
1873	+	sprintf(painCave.errMsg,
1874	+	"SimSetup error: If you use an NPT\n"
1875	+	"\tensemble, you must set tauThermostat.\n");
1876	+	painCave.isFatal = 1;
1877	+	simError();
1878	+	}
1879	+
1880	+	if (globals->haveTauBarostat())
1881	+	myNPTi->setTauBarostat(globals->getTauBarostat());
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 = myNPTi;
1891	+	break;
1892	+
1893	+	case NPTf_ENS:
1894	+	if (globals->haveZconstraints()){
1895	+	setupZConstraint(info[k]);
1896	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	+	}
1898	+	else
1899	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	+
1901	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1902	+
1903	+	if (globals->haveTargetPressure())
1904	+	myNPTf->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	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1915	+
1916	+	else{
1917	+	sprintf(painCave.errMsg,
1918	+	"SimSetup error: If you use an NPT\n"
1919	+	"\tensemble, you must set tauThermostat.\n");
1920	+	painCave.isFatal = 1;
1921	+	simError();
1922	+	}
1923	+
1924	+	if (globals->haveTauBarostat())
1925	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1926	+
1927	+	else{
1928	+	sprintf(painCave.errMsg,
1929	+	"SimSetup error: If you use an NPT\n"
1930	+	"\tensemble, you must set tauBarostat.\n");
1931	+	painCave.isFatal = 1;
1932	+	simError();
1933	+	}
1934	+
1935	+	info->the_integrator = myNPTf;
1936	+	break;
1937	+
1938	+	case NPTxyz_ENS:
1939	+	if (globals->haveZconstraints()){
1940	+	setupZConstraint(info[k]);
1941	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1942	+	}
1943	+	else
1944	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1945	+
1946	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1947	+
1948	+	if (globals->haveTargetPressure())
1949	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1950	+	else{
1951	+	sprintf(painCave.errMsg,
1952	+	"SimSetup error: If you use a constant pressure\n"
1953	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1954	+	painCave.isFatal = 1;
1955	+	simError();
1956	+	}
1957	+
1958	+	if (globals->haveTauThermostat())
1959	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1960	+	else{
1961	+	sprintf(painCave.errMsg,
1962	+	"SimSetup error: If you use an NPT\n"
1963	+	"\tensemble, you must set tauThermostat.\n");
1964	+	painCave.isFatal = 1;
1965	+	simError();
1966	+	}
1967	+
1968	+	if (globals->haveTauBarostat())
1969	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1970	+	else{
1971	+	sprintf(painCave.errMsg,
1972	+	"SimSetup error: If you use an NPT\n"
1973	+	"\tensemble, you must set tauBarostat.\n");
1974	+	painCave.isFatal = 1;
1975	+	simError();
1976	+	}
1977	+
1978	+	info->the_integrator = myNPTxyz;
1979	+	break;
1980	+
1981	+	default:
1982	+	sprintf(painCave.errMsg,
1983	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1984	+	painCave.isFatal = 1;
1985	+	simError();
1986	+	}
1987	+	}
1988	+	}
1989	+
1990	+	void SimSetup::initFortran(void){
1991	+	info[0].refreshSim();
1992	+
1993	+	if (!strcmp(info[0].mixingRule, "standard")){
1994	+	the_ff->initForceField(LB_MIXING_RULE);
1995	+	}
1996	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1997	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1998	+	}
1999	+	else{
2000	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2001	+	info[0].mixingRule);
2002	+	painCave.isFatal = 1;
2003	+	simError();
2004	+	}
2005	+
2006	+
2007	+	#ifdef IS_MPI
2008	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2009	+	MPIcheckPoint();
2010	+	#endif // is_mpi
2011	+	}
2012	+
2013	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2014	+	int nZConstraints;
2015	+	ZconStamp** zconStamp;
2016	+
2017	+	if (globals->haveZconstraintTime()){
2018	+	//add sample time of z-constraint  into SimInfo's property list
2019	+	DoubleData* zconsTimeProp = new DoubleData();
2020	+	zconsTimeProp->setID(ZCONSTIME_ID);
2021	+	zconsTimeProp->setData(globals->getZconsTime());
2022	+	theInfo.addProperty(zconsTimeProp);
2023	+	}
2024	+	else{
2025	+	sprintf(painCave.errMsg,
2026	+	"ZConstraint error: If you use a ZConstraint,\n"
2027	+	"\tyou must set zconsTime.\n");
2028	+	painCave.isFatal = 1;
2029	+	simError();
2030	+	}
2031	+
2032	+	//push zconsTol into siminfo, if user does not specify
2033	+	//value for zconsTol, a default value will be used
2034	+	DoubleData* zconsTol = new DoubleData();
2035	+	zconsTol->setID(ZCONSTOL_ID);
2036	+	if (globals->haveZconsTol()){
2037	+	zconsTol->setData(globals->getZconsTol());
2038	+	}
2039	+	else{
2040	+	double defaultZConsTol = 0.01;
2041	+	sprintf(painCave.errMsg,
2042	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2043	+	"\tOOPSE will use a default value of %f.\n"
2044	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2045	+	defaultZConsTol);
2046	+	painCave.isFatal = 0;
2047	+	simError();
2048	+
2049	+	zconsTol->setData(defaultZConsTol);
2050	+	}
2051	+	theInfo.addProperty(zconsTol);
2052	+
2053	+	//set Force Subtraction Policy
2054	+	StringData* zconsForcePolicy = new StringData();
2055	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2056	+
2057	+	if (globals->haveZconsForcePolicy()){
2058	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2059	+	}
2060	+	else{
2061	+	sprintf(painCave.errMsg,
2062	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2063	+	"\tOOPSE will use PolicyByMass.\n"
2064	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2065	+	painCave.isFatal = 0;
2066	+	simError();
2067	+	zconsForcePolicy->setData("BYMASS");
2068	+	}
2069	+
2070	+	theInfo.addProperty(zconsForcePolicy);
2071	+
2072	+	//set zcons gap
2073	+	DoubleData* zconsGap = new DoubleData();
2074	+	zconsGap->setID(ZCONSGAP_ID);
2075	+
2076	+	if (globals->haveZConsGap()){
2077	+	zconsGap->setData(globals->getZconsGap());
2078	+	theInfo.addProperty(zconsGap);
2079	+	}
2080	+
2081	+	//set zcons fixtime
2082	+	DoubleData* zconsFixtime = new DoubleData();
2083	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2084	+
2085	+	if (globals->haveZConsFixTime()){
2086	+	zconsFixtime->setData(globals->getZconsFixtime());
2087	+	theInfo.addProperty(zconsFixtime);
2088	+	}
2089	+
2090	+	//set zconsUsingSMD
2091	+	IntData* zconsUsingSMD = new IntData();
2092	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2093	+
2094	+	if (globals->haveZConsUsingSMD()){
2095	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2096	+	theInfo.addProperty(zconsUsingSMD);
2097	+	}
2098	+
2099	+	//Determine the name of ouput file and add it into SimInfo's property list
2100	+	//Be careful, do not use inFileName, since it is a pointer which
2101	+	//point to a string at master node, and slave nodes do not contain that string
2102	+
2103	+	string zconsOutput(theInfo.finalName);
2104	+
2105	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2106	+
2107	+	StringData* zconsFilename = new StringData();
2108	+	zconsFilename->setID(ZCONSFILENAME_ID);
2109	+	zconsFilename->setData(zconsOutput);
2110	+
2111	+	theInfo.addProperty(zconsFilename);
2112	+
2113	+	//setup index, pos and other parameters of z-constraint molecules
2114	+	nZConstraints = globals->getNzConstraints();
2115	+	theInfo.nZconstraints = nZConstraints;
2116	+
2117	+	zconStamp = globals->getZconStamp();
2118	+	ZConsParaItem tempParaItem;
2119	+
2120	+	ZConsParaData* zconsParaData = new ZConsParaData();
2121	+	zconsParaData->setID(ZCONSPARADATA_ID);
2122	+
2123	+	for (int i = 0; i < nZConstraints; i++){
2124	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2125	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2126	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2127	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2128	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2129	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2130	+	zconsParaData->addItem(tempParaItem);
2131	+	}
2132	+
2133	+	//check the uniqueness of index
2134	+	if(!zconsParaData->isIndexUnique()){
2135	+	sprintf(painCave.errMsg,
2136	+	"ZConstraint Error: molIndex is not unique!\n");
2137	+	painCave.isFatal = 1;
2138	+	simError();
2139	+	}
2140	+
2141	+	//sort the parameters by index of molecules
2142	+	zconsParaData->sortByIndex();
2143	+
2144	+	//push data into siminfo, therefore, we can retrieve later
2145	+	theInfo.addProperty(zconsParaData);
2146	+	}
2147	+
2148	+	void SimSetup::makeMinimizer(){
2149	+
2150	+	OOPSEMinimizer* myOOPSEMinimizer;
2151	+	MinimizerParameterSet* param;
2152	+	char minimizerName[100];
2153	+
2154	+	for (int i = 0; i < nInfo; i++){
2155	+
2156	+	//prepare parameter set for minimizer
2157	+	param = new MinimizerParameterSet();
2158	+	param->setDefaultParameter();
2159	+
2160	+	if (globals->haveMinimizer()){
2161	+	param->setFTol(globals->getMinFTol());
2162	+	}
2163	+
2164	+	if (globals->haveMinGTol()){
2165	+	param->setGTol(globals->getMinGTol());
2166	+	}
2167	+
2168	+	if (globals->haveMinMaxIter()){
2169	+	param->setMaxIteration(globals->getMinMaxIter());
2170	+	}
2171	+
2172	+	if (globals->haveMinWriteFrq()){
2173	+	param->setMaxIteration(globals->getMinMaxIter());
2174	+	}
2175	+
2176	+	if (globals->haveMinWriteFrq()){
2177	+	param->setWriteFrq(globals->getMinWriteFrq());
2178	+	}
2179	+
2180	+	if (globals->haveMinStepSize()){
2181	+	param->setStepSize(globals->getMinStepSize());
2182	+	}
2183	+
2184	+	if (globals->haveMinLSMaxIter()){
2185	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinLSTol()){
2189	+	param->setLineSearchTol(globals->getMinLSTol());
2190	+	}
2191	+
2192	+	strcpy(minimizerName, globals->getMinimizer());
2193	+
2194	+	if (!strcasecmp(minimizerName, "CG")){
2195	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2196	+	}
2197	+	else if (!strcasecmp(minimizerName, "SD")){
2198	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2199	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2200	+	}
2201	+	else{
2202	+	sprintf(painCave.errMsg,
2203	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2204	+	painCave.isFatal = 0;
2205	+	simError();
2206	+
2207	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2208	+	}
2209	+	info[i].the_integrator = myOOPSEMinimizer;
2210	+
2211	+	//store the minimizer into simInfo
2212	+	info[i].the_minimizer = myOOPSEMinimizer;
2213	+	info[i].has_minimizer = true;
2214	+	}
2215	+
2216	+	}

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