ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 1116 by tim, Thu Apr 15 22:15:21 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
18		#include "mpiSimulation.hpp"
19		#endif
20
21	+	// some defines for ensemble and Forcefield  cases
22	+
23	+	#define NVE_ENS        0
24	+	#define NVT_ENS        1
25	+	#define NPTi_ENS       2
26	+	#define NPTf_ENS       3
27	+	#define NPTxyz_ENS     4
28	+
29	+
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35	+	using namespace std;
36	+
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 27 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	// get the ensemble and set up an extended system if we need it:
135	<	strcpy( ensemble, the_globals->getEnsemble() );
136	<	if( !strcasecmp( ensemble, "NPT" ) ) {
137	<	the_extendedsystem = new ExtendedSystem( simnfo );
138	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
139	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
140	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
141	<	the_extendedsystem = new ExtendedSystem( simnfo );
142	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
143	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
144	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
134	>	// check on the post processing info
135	>
136	>	finalInfoCheck();
137	>
138	>	// initialize the system coordinates
139	>
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142	>
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
104	–	strcpy( simnfo->ensemble, ensemble );
146
147	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111	<	else{
112	<	sprintf( painCave.errMsg,
113	<	"SimSetup Error. Unrecognized force field -> %s\n",
114	<	force_field );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
147	>	// make the output filenames
148
149	+	makeOutNames();
150	+
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "ForceField creation successful" );
153	<	MPIcheckPoint();
122	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<
155	>	// initialize the Fortran
156
157	<	// get the components and calculate the tot_nMol and indvidual n_mol
127	<	the_components = the_globals->getComponents();
128	<	components_nmol = new int[n_components];
129	<	comp_stamps = new MoleculeStamp*[n_components];
157	>	initFortran();
158
159	<	if( !the_globals->haveNMol() ){
160	<	// we don't have the total number of molecules, so we assume it is
161	<	// given in each component
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	tot_nmol = 0;
136	<	for( i=0; i<n_components; i++ ){
166	>	}
167
138	–	if( !the_components[i]->haveNMol() ){
139	–	// we have a problem
140	–	sprintf( painCave.errMsg,
141	–	"SimSetup Error. No global NMol or component NMol"
142	–	" given. Cannot calculate the number of atoms.\n" );
143	–	painCave.isFatal = 1;
144	–	simError();
145	–	}
168
169	<	tot_nmol += the_components[i]->getNMol();
170	<	components_nmol[i] = the_components[i]->getNMol();
171	<	}
172	<	}
173	<	else{
174	<	sprintf( painCave.errMsg,
175	<	"SimSetup error.\n"
176	<	"\tSorry, the ability to specify total"
177	<	" nMols and then give molfractions in the components\n"
178	<	"\tis not currently supported."
179	<	" Please give nMol in the components.\n" );
180	<	painCave.isFatal = 1;
181	<	simError();
182	<
183	<
184	<	//     tot_nmol = the_globals->getNMol();
185	<
164	<	//   //we have the total number of molecules, now we check for molfractions
165	<	//     for( i=0; i<n_components; i++ ){
166	<
167	<	//       if( !the_components[i]->haveMolFraction() ){
168	<
169	<	//  if( !the_components[i]->haveNMol() ){
170	<	//    //we have a problem
171	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
172	<	//              << " nMol was given in component
173	<
174	<	}
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186
187	<	#ifdef IS_MPI
188	<	strcpy( checkPointMsg, "Have the number of components" );
189	<	MPIcheckPoint();
179	<	#endif // is_mpi
187	>	bond_pair* theBonds;
188	>	bend_set* theBends;
189	>	torsion_set* theTorsions;
190
191	<	// make an array of molecule stamps that match the components used.
182	<	// also extract the used stamps out into a separate linked list
191	>	set<int> skipList;
192
193	<	simnfo->nComponents = n_components;
194	<	simnfo->componentsNmol = components_nmol;
195	<	simnfo->compStamps = comp_stamps;
187	<	simnfo->headStamp = new LinkedMolStamp();
188	<
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
192	<	for( i=0; i<n_components; i++ ){
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196
197	<	id = the_components[i]->getType();
195	<	comp_stamps[i] = NULL;
196	<
197	<	// check to make sure the component isn't already in the list
197	>	//init the forceField paramters
198
199	<	comp_stamps[i] = headStamp->match( id );
200	<	if( comp_stamps[i] == NULL ){
201	<
202	<	// extract the component from the list;
203	<
204	<	currentStamp = the_stamps->extractMolStamp( id );
205	<	if( currentStamp == NULL ){
206	<	sprintf( painCave.errMsg,
207	<	"SimSetup error: Component \"%s\" was not found in the "
208	<	"list of declared molecules\n",
209	<	id );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	headStamp->add( currentStamp );
215	<	comp_stamps[i] = headStamp->match( id );
216	<	}
217	<	}
199	>	the_ff->readParams();
200
201	<	#ifdef IS_MPI
220	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
221	<	MPIcheckPoint();
222	<	#endif // is_mpi
223	<
201	>	// init the atoms
202
203	+	int nMembers, nNew, rb1, rb2;
204
205	<
206	<	// caclulate the number of atoms, bonds, bends and torsions
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207
208	<	tot_atoms = 0;
230	<	tot_bonds = 0;
231	<	tot_bends = 0;
232	<	tot_torsions = 0;
233	<	for( i=0; i<n_components; i++ ){
234	<
235	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
236	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
237	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
238	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
239	<	}
208	>	atomOffset = 0;
209
210	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213
214	<	simnfo->n_atoms = tot_atoms;
215	<	simnfo->n_bonds = tot_bonds;
216	<	simnfo->n_bends = tot_bends;
217	<	simnfo->n_torsions = tot_torsions;
218	<	simnfo->n_SRI = tot_SRI;
219	<	simnfo->n_mol = tot_nmol;
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221
222	<
223	<	#ifdef IS_MPI
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226
227	<	// divide the molecules among processors here.
228	<
229	<	mpiSim = new mpiSimulation( simnfo );
230	<
257	<
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231
232	<	globalIndex = mpiSim->divideLabor();
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236
237	<	// set up the local variables
238	<
239	<	int localMol, allMol;
264	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
265	<
266	<	int* mol2proc = mpiSim->getMolToProcMap();
267	<	int* molCompType = mpiSim->getMolComponentType();
268	<
269	<	allMol = 0;
270	<	localMol = 0;
271	<	local_atoms = 0;
272	<	local_bonds = 0;
273	<	local_bends = 0;
274	<	local_torsions = 0;
275	<	for( i=0; i<n_components; i++ ){
276	<
277	<	for( j=0; j<components_nmol[i]; j++ ){
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	if( mol2proc[j] == worldRank ){
280	<
281	<	local_atoms +=    comp_stamps[i]->getNAtoms();
282	<	local_bonds +=    comp_stamps[i]->getNBonds();
283	<	local_bends +=    comp_stamps[i]->getNBends();
284	<	local_torsions += comp_stamps[i]->getNTorsions();
285	<	localMol++;
286	<	}
287	<	allMol++;
288	<	}
289	<	}
290	<	local_SRI = local_bonds + local_bends + local_torsions;
291	<
241	>	// make the Atoms
242
243	<	simnfo->n_atoms = mpiSim->getMyNlocal();
244	<
295	<	if( local_atoms != simnfo->n_atoms ){
296	<	sprintf( painCave.errMsg,
297	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
298	<	" localAtom (%d) are not equal.\n",
299	<	simnfo->n_atoms,
300	<	local_atoms );
301	<	painCave.isFatal = 1;
302	<	simError();
303	<	}
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245
246	<	simnfo->n_bonds = local_bonds;
247	<	simnfo->n_bends = local_bends;
248	<	simnfo->n_torsions = local_torsions;
249	<	simnfo->n_SRI = local_SRI;
250	<	simnfo->n_mol = localMol;
246	>	if (currentAtom->haveOrientation()){
247	>	dAtom = new DirectionalAtom((j + atomOffset),
248	>	info[k].getConfiguration());
249	>	info[k].n_oriented++;
250	>	molInfo.myAtoms[j] = dAtom;
251
252	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
253	<	MPIcheckPoint();
254	<
314	<
315	<	#endif // is_mpi
316	<
252	>	// Directional Atoms have standard unit vectors which are oriented
253	>	// in space using the three Euler angles.  We assume the standard
254	>	// unit vector was originally along the z axis below.
255
256	<	// create the atom and short range interaction arrays
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	Atom::createArrays(simnfo->n_atoms);
261	<	the_atoms = new Atom*[simnfo->n_atoms];
262	<	the_molecules = new Molecule[simnfo->n_mol];
263	<	int molIndex;
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	<	// initialize the molecule's stampID's
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
267	+	}
268	+
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
328	–
271
272	<	molIndex = 0;
331	<	for(i=0; i<mpiSim->getTotNmol(); i++){
332	<
333	<	if(mol2proc[i] == worldRank ){
334	<	the_molecules[molIndex].setStampID( molCompType[i] );
335	<	the_molecules[molIndex].setMyIndex( molIndex );
336	<	molIndex++;
337	<	}
338	<	}
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
340	–	#else // is_mpi
341	–
342	–	molIndex = 0;
343	–	for(i=0; i<n_components; i++){
344	–	for(j=0; j<components_nmol[i]; j++ ){
345	–	the_molecules[molIndex].setStampID( i );
346	–	the_molecules[molIndex].setMyIndex( molIndex );
347	–	molIndex++;
348	–	}
349	–	}
350	–
351	–
274		#endif // is_mpi
275	+	}
276
277	+	// make the bonds
278	+	for (j = 0; j < molInfo.nBonds; j++){
279	+	currentBond = comp_stamps[stampID]->getBond(j);
280	+	theBonds[j].a = currentBond->getA() + atomOffset;
281	+	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	<	if( simnfo->n_SRI ){
284	<
357	<	Exclude::createArray(simnfo->n_SRI);
358	<	the_excludes = new Exclude*[simnfo->n_SRI];
359	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360	<	simnfo->globalExcludes = new int;
361	<	simnfo->n_exclude = simnfo->n_SRI;
362	<	}
363	<	else{
364	<
365	<	Exclude::createArray( 1 );
366	<	the_excludes = new Exclude*;
367	<	the_excludes[0] = new Exclude(0);
368	<	the_excludes[0]->setPair( 0,0 );
369	<	simnfo->globalExcludes = new int;
370	<	simnfo->globalExcludes[0] = 0;
371	<	simnfo->n_exclude = 0;
372	<	}
283	>	tempI = theBonds[j].a;
284	>	tempJ = theBonds[j].b;
285
286	<	// set the arrays into the SimInfo object
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	simnfo->atoms = the_atoms;
295	<	simnfo->molecules = the_molecules;
378	<	simnfo->nGlobalExcludes = 0;
379	<	simnfo->excludes = the_excludes;
294	>	info[k].excludes->addPair(exI, exJ);
295	>	}
296
297	+	//make the bends
298	+	for (j = 0; j < molInfo.nBends; j++){
299	+	currentBend = comp_stamps[stampID]->getBend(j);
300	+	theBends[j].a = currentBend->getA() + atomOffset;
301	+	theBends[j].b = currentBend->getB() + atomOffset;
302	+	theBends[j].c = currentBend->getC() + atomOffset;
303
304	<	// get some of the tricky things that may still be in the globals
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<
309	<	if( the_globals->haveBox() ){
310	<	simnfo->box_x = the_globals->getBox();
311	<	simnfo->box_y = the_globals->getBox();
312	<	simnfo->box_z = the_globals->getBox();
313	<	}
314	<	else if( the_globals->haveDensity() ){
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315
316	<	double vol;
317	<	vol = (double)tot_nmol / the_globals->getDensity();
318	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
319	<	simnfo->box_y = simnfo->box_x;
320	<	simnfo->box_z = simnfo->box_x;
397	<	}
398	<	else{
399	<	if( !the_globals->haveBoxX() ){
400	<	sprintf( painCave.errMsg,
401	<	"SimSetup error, no periodic BoxX size given.\n" );
402	<	painCave.isFatal = 1;
403	<	simError();
404	<	}
405	<	simnfo->box_x = the_globals->getBoxX();
406	<
407	<	if( !the_globals->haveBoxY() ){
408	<	sprintf( painCave.errMsg,
409	<	"SimSetup error, no periodic BoxY size given.\n" );
410	<	painCave.isFatal = 1;
411	<	simError();
412	<	}
413	<	simnfo->box_y = the_globals->getBoxY();
414	<
415	<	if( !the_globals->haveBoxZ() ){
416	<	sprintf( painCave.errMsg,
417	<	"SimSetup error, no periodic BoxZ size given.\n" );
418	<	painCave.isFatal = 1;
419	<	simError();
420	<	}
421	<	simnfo->box_z = the_globals->getBoxZ();
422	<	}
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	#ifdef IS_MPI
323	<	strcpy( checkPointMsg, "Box size set up" );
324	<	MPIcheckPoint();
325	<	#endif // is_mpi
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340
341	+	current_extra = current_extra->getNext();
342	+	}
343	+	}
344
345	<	// initialize the arrays
345	>	if (theBends[j].isGhost) {
346	>
347	>	tempI = theBends[j].a;
348	>	tempJ = theBends[j].b;
349	>
350	>	#ifdef IS_MPI
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	the_ff->setSimInfo( simnfo );
359	>	} else {
360
361	<	makeMolecules();
362	<	simnfo->identArray = new int[simnfo->n_atoms];
363	<	for(i=0; i<simnfo->n_atoms; i++){
364	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
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;
452	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
453	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
454	<	simnfo->ecr = 0.5 * smallest;
455	<	} else {
456	<	simnfo->ecr        = the_globals->getECR();
457	<	}
458	<
459	<	if( !the_globals->haveEST() ){
460	<	sprintf( painCave.errMsg,
461	<	"SimSetup Warning: using default value of 0.05 * the "
462	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
463	<	);
464	<	painCave.isFatal = 0;
465	<	simError();
466	<	simnfo->est = 0.05 * simnfo->ecr;
467	<	} else {
468	<	simnfo->est        = the_globals->getEST();
469	<	}
470	<
471	<	if(!the_globals->haveDielectric() ){
472	<	sprintf( painCave.errMsg,
473	<	"SimSetup Error: You are trying to use Reaction Field without"
474	<	"setting a dielectric constant!\n"
475	<	);
476	<	painCave.isFatal = 1;
477	<	simError();
478	<	}
479	<	simnfo->dielectric = the_globals->getDielectric();
480	<	} else {
481	<	if (simnfo->n_dipoles) {
482	<
483	<	if( !the_globals->haveECR() ){
484	<	sprintf( painCave.errMsg,
485	<	"SimSetup Warning: using default value of 1/2 the smallest"
486	<	"box length for the electrostaticCutoffRadius.\n"
487	<	"I hope you have a very fast processor!\n");
488	<	painCave.isFatal = 0;
489	<	simError();
490	<	double smallest;
491	<	smallest = simnfo->box_x;
492	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
493	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
494	<	simnfo->ecr = 0.5 * smallest;
495	<	} else {
496	<	simnfo->ecr        = the_globals->getECR();
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
498	–
499	–	if( !the_globals->haveEST() ){
500	–	sprintf( painCave.errMsg,
501	–	"SimSetup Warning: using default value of 5% of the"
502	–	"electrostaticCutoffRadius for the "
503	–	"electrostaticSkinThickness\n"
504	–	);
505	–	painCave.isFatal = 0;
506	–	simError();
507	–	simnfo->est = 0.05 * simnfo->ecr;
508	–	} else {
509	–	simnfo->est        = the_globals->getEST();
510	–	}
511	–	}
512	–	}
380
381	<	#ifdef IS_MPI
382	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
383	<	MPIcheckPoint();
384	<	#endif // is_mpi
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	<	if( the_globals->haveInitialConfig() ){
389	<
390	<	InitializeFromFile* fileInit;
391	<	#ifdef IS_MPI // is_mpi
392	<	if( worldRank == 0 ){
524	<	#endif //is_mpi
525	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
388	>	tempI = theTorsions[j].a;
389	>	tempJ = theTorsions[j].b;
390	>	tempK = theTorsions[j].c;
391	>	tempL = theTorsions[j].d;
392	>
393		#ifdef IS_MPI
394	<	}else fileInit = new InitializeFromFile( NULL );
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403		#endif
529	–	fileInit->read_xyz( simnfo ); // default velocities on
404
405	<	delete fileInit;
406	<	}
407	<	else{
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	#ifdef IS_MPI
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	<	// no init from bass
419	<
539	<	sprintf( painCave.errMsg,
540	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
541	<	painCave.isFatal;
542	<	simError();
543	<
544	<	#else
418	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	>	nMembers = currentRigidBody->getNMembers();
420
421	<	initFromBass();
421	>	// Create the Rigid Body:
422
423	+	myRB = new RigidBody();
424
425	<	#endif
426	<	}
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429
430	<	#ifdef IS_MPI
431	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
554	<	MPIcheckPoint();
555	<	#endif // is_mpi
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432
433	+	// tempI is atom numbering on local processor
434	+	tempI = molI + atomOffset;
435
436	<
437	<
438	<
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439
440	<
440	>	// When we add to the rigid body, add the atom itself and
441	>	// the stamp info:
442	>
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446		#ifdef IS_MPI
447	<	if( worldRank == 0 ){
448	<	#endif // is_mpi
449	<
450	<	if( the_globals->haveFinalConfig() ){
451	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
452	<	}
453	<	else{
454	<	strcpy( simnfo->finalName, inFileName );
455	<	char* endTest;
456	<	int nameLength = strlen( simnfo->finalName );
457	<	endTest = &(simnfo->finalName[nameLength - 5]);
458	<	if( !strcmp( endTest, ".bass" ) ){
459	<	strcpy( endTest, ".eor" );
460	<	}
461	<	else if( !strcmp( endTest, ".BASS" ) ){
462	<	strcpy( endTest, ".eor" );
463	<	}
464	<	else{
465	<	endTest = &(simnfo->finalName[nameLength - 4]);
583	<	if( !strcmp( endTest, ".bss" ) ){
584	<	strcpy( endTest, ".eor" );
585	<	}
586	<	else if( !strcmp( endTest, ".mdl" ) ){
587	<	strcpy( endTest, ".eor" );
588	<	}
589	<	else{
590	<	strcat( simnfo->finalName, ".eor" );
591	<	}
592	<	}
593	<	}
594	<
595	<	// make the sample and status out names
596	<
597	<	strcpy( simnfo->sampleName, inFileName );
598	<	char* endTest;
599	<	int nameLength = strlen( simnfo->sampleName );
600	<	endTest = &(simnfo->sampleName[nameLength - 5]);
601	<	if( !strcmp( endTest, ".bass" ) ){
602	<	strcpy( endTest, ".dump" );
603	<	}
604	<	else if( !strcmp( endTest, ".BASS" ) ){
605	<	strcpy( endTest, ".dump" );
606	<	}
607	<	else{
608	<	endTest = &(simnfo->sampleName[nameLength - 4]);
609	<	if( !strcmp( endTest, ".bss" ) ){
610	<	strcpy( endTest, ".dump" );
611	<	}
612	<	else if( !strcmp( endTest, ".mdl" ) ){
613	<	strcpy( endTest, ".dump" );
614	<	}
615	<	else{
616	<	strcat( simnfo->sampleName, ".dump" );
617	<	}
618	<	}
619	<
620	<	strcpy( simnfo->statusName, inFileName );
621	<	nameLength = strlen( simnfo->statusName );
622	<	endTest = &(simnfo->statusName[nameLength - 5]);
623	<	if( !strcmp( endTest, ".bass" ) ){
624	<	strcpy( endTest, ".stat" );
625	<	}
626	<	else if( !strcmp( endTest, ".BASS" ) ){
627	<	strcpy( endTest, ".stat" );
628	<	}
629	<	else{
630	<	endTest = &(simnfo->statusName[nameLength - 4]);
631	<	if( !strcmp( endTest, ".bss" ) ){
632	<	strcpy( endTest, ".stat" );
633	<	}
634	<	else if( !strcmp( endTest, ".mdl" ) ){
635	<	strcpy( endTest, ".stat" );
636	<	}
637	<	else{
638	<	strcat( simnfo->statusName, ".stat" );
639	<	}
640	<	}
641	<
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466		#ifdef IS_MPI
467	<	}
468	<	#endif // is_mpi
469	<
470	<	// set the status, sample, and themal kick times
471	<
472	<	if( the_globals->haveSampleTime() ){
473	<	simnfo->sampleTime = the_globals->getSampleTime();
474	<	simnfo->statusTime = simnfo->sampleTime;
475	<	simnfo->thermalTime = simnfo->sampleTime;
476	<	}
477	<	else{
654	<	simnfo->sampleTime = the_globals->getRunTime();
655	<	simnfo->statusTime = simnfo->sampleTime;
656	<	simnfo->thermalTime = simnfo->sampleTime;
657	<	}
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	<	if( the_globals->haveStatusTime() ){
480	<	simnfo->statusTime = the_globals->getStatusTime();
481	<	}
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481	>	}
482	>
483
484	<	if( the_globals->haveThermalTime() ){
485	<	simnfo->thermalTime = the_globals->getThermalTime();
665	<	}
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486
487	<	// check for the temperature set flag
487	>	molInfo.myIntegrableObjects.clear();
488	>
489
490	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491
492	+	#ifdef IS_MPI
493	+	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	+	#else
495	+	slJ = j+atomOffset;
496	+	#endif
497
498	<	//   // make the longe range forces and the integrator
498	>	// if they aren't on the skip list, then they can be integrated
499
500	<	//   new AllLong( simnfo );
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505	>	}
506
507	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677	<	the_ff,
678	<	the_extendedsystem);
679	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680	<	the_ff,
681	<	the_extendedsystem );
507	>	// all rigid bodies are integrated:
508
509	<	#ifdef IS_MPI
510	<	mpiSim->mpiRefresh();
511	<	#endif
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513	>	}
514	>
515	>
516	>	// send the arrays off to the forceField for init.
517	>
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523
524	<	// initialize the Fortran
524	>	info[k].molecules[i].initialize(molInfo);
525
526
527	<	simnfo->refreshSim();
528	<
529	<	if( !strcmp( simnfo->mixingRule, "standard") ){
530	<	the_ff->initForceField( LB_MIXING_RULE );
527	>	atomOffset += molInfo.nAtoms;
528	>	delete[] theBonds;
529	>	delete[] theBends;
530	>	delete[] theTorsions;
531	>	}
532		}
695	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
696	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
697	–	}
698	–	else{
699	–	sprintf( painCave.errMsg,
700	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
701	–	simnfo->mixingRule );
702	–	painCave.isFatal = 1;
703	–	simError();
704	–	}
533
706	–
534		#ifdef IS_MPI
535	<	strcpy( checkPointMsg,
709	<	"Successfully intialized the mixingRule for Fortran." );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
712	–	}
538
539	+	// clean up the forcefield
540
541	<	void SimSetup::makeMolecules( void ){
541	>	if (!globals->haveLJrcut()){
542
543	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
718	<	molInit info;
719	<	DirectionalAtom* dAtom;
720	<	LinkedAssign* extras;
721	<	LinkedAssign* current_extra;
722	<	AtomStamp* currentAtom;
723	<	BondStamp* currentBond;
724	<	BendStamp* currentBend;
725	<	TorsionStamp* currentTorsion;
543	>	the_ff->calcRcut();
544
545	<	bond_pair* theBonds;
546	<	bend_set* theBends;
547	<	torsion_set* theTorsions;
545	>	} else {
546	>
547	>	the_ff->setRcut( globals->getLJrcut() );
548	>	}
549
550	<
551	<	//init the forceField paramters
550	>	the_ff->cleanMe();
551	>	}
552
553	<	the_ff->readParams();
553	>	void SimSetup::initFromBass(void){
554	>	int i, j, k;
555	>	int n_cells;
556	>	double cellx, celly, cellz;
557	>	double temp1, temp2, temp3;
558	>	int n_per_extra;
559	>	int n_extra;
560	>	int have_extra, done;
561
562	<
563	<	// init the atoms
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	double ux, uy, uz, u, uSqr;
568	<
569	<	atomOffset = 0;
742	<	excludeOffset = 0;
743	<	for(i=0; i<simnfo->n_mol; i++){
744	<
745	<	stampID = the_molecules[i].getStampID();
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
572	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
573	<	info.nBends    = comp_stamps[stampID]->getNBends();
574	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
751	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
571	>	have_extra = 0;
572	>	if (temp2 < temp3){
573	>	// we have a non-complete lattice
574	>	have_extra = 1;
575
576	<	info.myAtoms = &the_atoms[atomOffset];
577	<	info.myExcludes = &the_excludes[excludeOffset];
578	<	info.myBonds = new Bond*[info.nBonds];
579	<	info.myBends = new Bend*[info.nBends];
580	<	info.myTorsions = new Torsion*[info.nTorsions];
576	>	n_cells = (int) temp3 - 1;
577	>	cellx = info[0].boxL[0] / temp3;
578	>	celly = info[0].boxL[1] / temp3;
579	>	cellz = info[0].boxL[2] / temp3;
580	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	>	n_per_extra = (int) ceil(temp1);
583
584	<	theBonds = new bond_pair[info.nBonds];
585	<	theBends = new bend_set[info.nBends];
586	<	theTorsions = new torsion_set[info.nTorsions];
587	<
763	<	// make the Atoms
764	<
765	<	for(j=0; j<info.nAtoms; j++){
766	<
767	<	currentAtom = comp_stamps[stampID]->getAtom( j );
768	<	if( currentAtom->haveOrientation() ){
769	<
770	<	dAtom = new DirectionalAtom(j + atomOffset);
771	<	simnfo->n_oriented++;
772	<	info.myAtoms[j] = dAtom;
773	<
774	<	ux = currentAtom->getOrntX();
775	<	uy = currentAtom->getOrntY();
776	<	uz = currentAtom->getOrntZ();
777	<
778	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
779	<
780	<	u = sqrt( uSqr );
781	<	ux = ux / u;
782	<	uy = uy / u;
783	<	uz = uz / u;
784	<
785	<	dAtom->setSUx( ux );
786	<	dAtom->setSUy( uy );
787	<	dAtom->setSUz( uz );
788	<	}
789	<	else{
790	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
791	<	}
792	<	info.myAtoms[j]->setType( currentAtom->getType() );
793	<
794	<	#ifdef IS_MPI
795	<
796	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
797	<
798	<	#endif // is_mpi
799	<	}
800	<
801	<	// make the bonds
802	<	for(j=0; j<info.nBonds; j++){
803	<
804	<	currentBond = comp_stamps[stampID]->getBond( j );
805	<	theBonds[j].a = currentBond->getA() + atomOffset;
806	<	theBonds[j].b = currentBond->getB() + atomOffset;
807	<
808	<	exI = theBonds[j].a;
809	<	exJ = theBonds[j].b;
810	<
811	<	// exclude_I must always be the smaller of the pair
812	<	if( exI > exJ ){
813	<	tempEx = exI;
814	<	exI = exJ;
815	<	exJ = tempEx;
816	<	}
817	<	#ifdef IS_MPI
818	<	tempEx = exI;
819	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
820	<	tempEx = exJ;
821	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
822	<
823	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
824	<	#else  // isn't MPI
825	<
826	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
827	<	#endif  //is_mpi
828	<	}
829	<	excludeOffset += info.nBonds;
830	<
831	<	//make the bends
832	<	for(j=0; j<info.nBends; j++){
833	<
834	<	currentBend = comp_stamps[stampID]->getBend( j );
835	<	theBends[j].a = currentBend->getA() + atomOffset;
836	<	theBends[j].b = currentBend->getB() + atomOffset;
837	<	theBends[j].c = currentBend->getC() + atomOffset;
838	<
839	<	if( currentBend->haveExtras() ){
840	<
841	<	extras = currentBend->getExtras();
842	<	current_extra = extras;
843	<
844	<	while( current_extra != NULL ){
845	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846	<
847	<	switch( current_extra->getType() ){
848	<
849	<	case 0:
850	<	theBends[j].ghost =
851	<	current_extra->getInt() + atomOffset;
852	<	theBends[j].isGhost = 1;
853	<	break;
854	<
855	<	case 1:
856	<	theBends[j].ghost =
857	<	(int)current_extra->getDouble() + atomOffset;
858	<	theBends[j].isGhost = 1;
859	<	break;
860	<
861	<	default:
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup Error: ghostVectorSource was neither a "
864	<	"double nor an int.\n"
865	<	"-->Bend[%d] in %s\n",
866	<	j, comp_stamps[stampID]->getID() );
867	<	painCave.isFatal = 1;
868	<	simError();
869	<	}
870	<	}
871	<
872	<	else{
873	<
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: unhandled bend assignment:\n"
876	<	"    -->%s in Bend[%d] in %s\n",
877	<	current_extra->getlhs(),
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<
883	<	current_extra = current_extra->getNext();
884	<	}
885	<	}
886	<
887	<	if( !theBends[j].isGhost ){
888	<
889	<	exI = theBends[j].a;
890	<	exJ = theBends[j].c;
891	<	}
892	<	else{
893	<
894	<	exI = theBends[j].a;
895	<	exJ = theBends[j].b;
896	<	}
897	<
898	<	// exclude_I must always be the smaller of the pair
899	<	if( exI > exJ ){
900	<	tempEx = exI;
901	<	exI = exJ;
902	<	exJ = tempEx;
903	<	}
904	<	#ifdef IS_MPI
905	<	tempEx = exI;
906	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907	<	tempEx = exJ;
908	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
909	<
910	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
911	<	#else  // isn't MPI
912	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913	<	#endif  //is_mpi
914	<	}
915	<	excludeOffset += info.nBends;
916	<
917	<	for(j=0; j<info.nTorsions; j++){
918	<
919	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
920	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
921	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
922	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
923	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
924	<
925	<	exI = theTorsions[j].a;
926	<	exJ = theTorsions[j].d;
927	<
928	<	// exclude_I must always be the smaller of the pair
929	<	if( exI > exJ ){
930	<	tempEx = exI;
931	<	exI = exJ;
932	<	exJ = tempEx;
933	<	}
934	<	#ifdef IS_MPI
935	<	tempEx = exI;
936	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
937	<	tempEx = exJ;
938	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
939	<
940	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
941	<	#else  // isn't MPI
942	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943	<	#endif  //is_mpi
944	<	}
945	<	excludeOffset += info.nTorsions;
946	<
947	<
948	<	// send the arrays off to the forceField for init.
949	<
950	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
951	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
952	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
953	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
954	<
955	<
956	<	the_molecules[i].initialize( info );
957	<
958	<
959	<	atomOffset += info.nAtoms;
960	<	delete[] theBonds;
961	<	delete[] theBends;
962	<	delete[] theTorsions;
963	<	}
964	<
965	<	#ifdef IS_MPI
966	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
967	<	MPIcheckPoint();
968	<	#endif // is_mpi
969	<
970	<	// clean up the forcefield
971	<	the_ff->calcRcut();
972	<	the_ff->cleanMe();
973	<
974	<	}
975	<
976	<	void SimSetup::initFromBass( void ){
977	<
978	<	int i, j, k;
979	<	int n_cells;
980	<	double cellx, celly, cellz;
981	<	double temp1, temp2, temp3;
982	<	int n_per_extra;
983	<	int n_extra;
984	<	int have_extra, done;
985	<
986	<	temp1 = (double)tot_nmol / 4.0;
987	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
988	<	temp3 = ceil( temp2 );
989	<
990	<	have_extra =0;
991	<	if( temp2 < temp3 ){ // we have a non-complete lattice
992	<	have_extra =1;
993	<
994	<	n_cells = (int)temp3 - 1;
995	<	cellx = simnfo->box_x / temp3;
996	<	celly = simnfo->box_y / temp3;
997	<	cellz = simnfo->box_z / temp3;
998	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
999	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1000	<	n_per_extra = (int)ceil( temp1 );
1001	<
1002	<	if( n_per_extra > 4){
1003	<	sprintf( painCave.errMsg,
1004	<	"SimSetup error. There has been an error in constructing"
1005	<	" the non-complete lattice.\n" );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588		painCave.isFatal = 1;
589		simError();
590		}
591		}
592		else{
593	<	n_cells = (int)temp3;
594	<	cellx = simnfo->box_x / temp3;
595	<	celly = simnfo->box_y / temp3;
596	<	cellz = simnfo->box_z / temp3;
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597		}
598
599		current_mol = 0;
#	Line 1019 | Line 601 | void SimSetup::initFromBass( void ){
601		current_comp = 0;
602		current_atom_ndx = 0;
603
604	<	for( i=0; i < n_cells ; i++ ){
605	<	for( j=0; j < n_cells; j++ ){
606	<	for( k=0; k < n_cells; k++ ){
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	makeElement( i * cellx,
1027	<	j * celly,
1028	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
1031	<	j * celly + 0.5 * celly,
1032	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	makeElement( i * cellx,
1035	<	j * celly + 0.5 * celly,
1036	<	k * cellz + 0.5 * cellz );
1037	<
1038	<	makeElement( i * cellx + 0.5 * cellx,
1039	<	j * celly,
1040	<	k * cellz + 0.5 * cellz );
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
615		}
616		}
617
618	<	if( have_extra ){
618	>	if (have_extra){
619		done = 0;
620
621		int start_ndx;
622	<	for( i=0; i < (n_cells+1) && !done; i++ ){
623	<	for( j=0; j < (n_cells+1) && !done; j++ ){
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	if( i < n_cells ){
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( j < n_cells ){
639	<	start_ndx = n_cells;
640	<	}
641	<	else start_ndx = 0;
642	<	}
1059	<	else start_ndx = 0;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	makeElement( i * cellx,
651	<	j * celly,
652	<	k * cellz );
653	<	done = ( current_mol >= tot_nmol );
654	<
655	<	if( !done && n_per_extra > 1 ){
1069	<	makeElement( i * cellx + 0.5 * cellx,
1070	<	j * celly + 0.5 * celly,
1071	<	k * cellz );
1072	<	done = ( current_mol >= tot_nmol );
1073	<	}
1074	<
1075	<	if( !done && n_per_extra > 2){
1076	<	makeElement( i * cellx,
1077	<	j * celly + 0.5 * celly,
1078	<	k * cellz + 0.5 * cellz );
1079	<	done = ( current_mol >= tot_nmol );
1080	<	}
1081	<
1082	<	if( !done && n_per_extra > 3){
1083	<	makeElement( i * cellx + 0.5 * cellx,
1084	<	j * celly,
1085	<	k * cellz + 0.5 * cellz );
1086	<	done = ( current_mol >= tot_nmol );
1087	<	}
1088	<	}
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657		}
658		}
659
660	<
661	<	for( i=0; i<simnfo->n_atoms; i++ ){
1095	<	simnfo->atoms[i]->set_vx( 0.0 );
1096	<	simnfo->atoms[i]->set_vy( 0.0 );
1097	<	simnfo->atoms[i]->set_vz( 0.0 );
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662		}
663		}
664
665	<	void SimSetup::makeElement( double x, double y, double z ){
1102	<
665	>	void SimSetup::makeElement(double x, double y, double z){
666		int k;
667		AtomStamp* current_atom;
668		DirectionalAtom* dAtom;
669		double rotMat[3][3];
670	+	double pos[3];
671
672	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
673	<
674	<	current_atom = comp_stamps[current_comp]->getAtom( k );
675	<	if( !current_atom->havePosition() ){
676	<	sprintf( painCave.errMsg,
677	<	"SimSetup:initFromBass error.\n"
678	<	"\tComponent %s, atom %s does not have a position specified.\n"
679	<	"\tThe initialization routine is unable to give a start"
680	<	" position.\n",
1117	<	comp_stamps[current_comp]->getID(),
1118	<	current_atom->getType() );
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
684
685	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
686	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
687	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1126	<
1127	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	+	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	+	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693	+
694		rotMat[0][0] = 1.0;
695		rotMat[0][1] = 0.0;
696		rotMat[0][2] = 0.0;
#	Line 1140 | Line 703 | void SimSetup::makeElement( double x, double y, double
703		rotMat[2][1] = 0.0;
704		rotMat[2][2] = 1.0;
705
706	<	dAtom->setA( rotMat );
706	>	dAtom->setA(rotMat);
707		}
708
709		current_atom_ndx++;
#	Line 1148 | Line 711 | void SimSetup::makeElement( double x, double y, double
711
712		current_mol++;
713		current_comp_mol++;
714	+
715	+	if (current_comp_mol >= components_nmol[current_comp]){
716	+	current_comp_mol = 0;
717	+	current_comp++;
718	+	}
719	+	}
720	+
721	+
722	+	void SimSetup::gatherInfo(void){
723	+	int i;
724	+
725	+	ensembleCase = -1;
726	+	ffCase = -1;
727	+
728	+	// set the easy ones first
729	+
730	+	for (i = 0; i < nInfo; i++){
731	+	info[i].target_temp = globals->getTargetTemp();
732	+	info[i].dt = globals->getDt();
733	+	info[i].run_time = globals->getRunTime();
734	+	}
735	+	n_components = globals->getNComponents();
736	+
737	+
738	+	// get the forceField
739	+
740	+	strcpy(force_field, globals->getForceField());
741	+
742	+	if (!strcasecmp(force_field, "DUFF")){
743	+	ffCase = FF_DUFF;
744	+	}
745	+	else if (!strcasecmp(force_field, "LJ")){
746	+	ffCase = FF_LJ;
747	+	}
748	+	else if (!strcasecmp(force_field, "EAM")){
749	+	ffCase = FF_EAM;
750	+	}
751	+	else if (!strcasecmp(force_field, "WATER")){
752	+	ffCase = FF_H2O;
753	+	}
754	+	else{
755	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	+	force_field);
757	+	painCave.isFatal = 1;
758	+	simError();
759	+	}
760	+
761	+	// get the ensemble
762	+
763	+	strcpy(ensemble, globals->getEnsemble());
764	+
765	+	if (!strcasecmp(ensemble, "NVE")){
766	+	ensembleCase = NVE_ENS;
767	+	}
768	+	else if (!strcasecmp(ensemble, "NVT")){
769	+	ensembleCase = NVT_ENS;
770	+	}
771	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772	+	ensembleCase = NPTi_ENS;
773	+	}
774	+	else if (!strcasecmp(ensemble, "NPTf")){
775	+	ensembleCase = NPTf_ENS;
776	+	}
777	+	else if (!strcasecmp(ensemble, "NPTxyz")){
778	+	ensembleCase = NPTxyz_ENS;
779	+	}
780	+	else{
781	+	sprintf(painCave.errMsg,
782	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	+	"\treverting to NVE for this simulation.\n",
784	+	ensemble);
785	+	painCave.isFatal = 0;
786	+	simError();
787	+	strcpy(ensemble, "NVE");
788	+	ensembleCase = NVE_ENS;
789	+	}
790	+
791	+	for (i = 0; i < nInfo; i++){
792	+	strcpy(info[i].ensemble, ensemble);
793	+
794	+	// get the mixing rule
795	+
796	+	strcpy(info[i].mixingRule, globals->getMixingRule());
797	+	info[i].usePBC = globals->getPBC();
798	+	}
799	+
800	+	// get the components and calculate the tot_nMol and indvidual n_mol
801	+
802	+	the_components = globals->getComponents();
803	+	components_nmol = new int[n_components];
804	+
805	+
806	+	if (!globals->haveNMol()){
807	+	// we don't have the total number of molecules, so we assume it is
808	+	// given in each component
809	+
810	+	tot_nmol = 0;
811	+	for (i = 0; i < n_components; i++){
812	+	if (!the_components[i]->haveNMol()){
813	+	// we have a problem
814	+	sprintf(painCave.errMsg,
815	+	"SimSetup Error. No global NMol or component NMol given.\n"
816	+	"\tCannot calculate the number of atoms.\n");
817	+	painCave.isFatal = 1;
818	+	simError();
819	+	}
820	+
821	+	tot_nmol += the_components[i]->getNMol();
822	+	components_nmol[i] = the_components[i]->getNMol();
823	+	}
824	+	}
825	+	else{
826	+	sprintf(painCave.errMsg,
827	+	"SimSetup error.\n"
828	+	"\tSorry, the ability to specify total"
829	+	" nMols and then give molfractions in the components\n"
830	+	"\tis not currently supported."
831	+	" Please give nMol in the components.\n");
832	+	painCave.isFatal = 1;
833	+	simError();
834	+	}
835	+
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time.  If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time.  If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time.  If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time.  If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876	+
877	+	// set the status, sample, and thermal kick times
878	+
879	+	for (i = 0; i < nInfo; i++){
880	+	if (globals->haveSampleTime()){
881	+	info[i].sampleTime = globals->getSampleTime();
882	+	info[i].statusTime = info[i].sampleTime;
883	+	info[i].thermalTime = info[i].sampleTime;
884	+	}
885	+	else{
886	+	info[i].sampleTime = globals->getRunTime();
887	+	info[i].statusTime = info[i].sampleTime;
888	+	info[i].thermalTime = info[i].sampleTime;
889	+	}
890	+
891	+	if (globals->haveStatusTime()){
892	+	info[i].statusTime = globals->getStatusTime();
893	+	}
894	+
895	+	if (globals->haveThermalTime()){
896	+	info[i].thermalTime = globals->getThermalTime();
897	+	}
898	+
899	+	info[i].resetIntegrator = 0;
900	+	if( globals->haveResetTime() ){
901	+	info[i].resetTime = globals->getResetTime();
902	+	info[i].resetIntegrator = 1;
903	+	}
904	+
905	+	// check for the temperature set flag
906	+
907	+	if (globals->haveTempSet())
908	+	info[i].setTemp = globals->getTempSet();
909	+
910	+	// check for the extended State init
911	+
912	+	info[i].useInitXSstate = globals->getUseInitXSstate();
913	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	+
915	+	}
916	+
917	+	//setup seed for random number generator
918	+	int seedValue;
919	+
920	+	if (globals->haveSeed()){
921	+	seedValue = globals->getSeed();
922	+
923	+	if(seedValue / 1E9 == 0){
924	+	sprintf(painCave.errMsg,
925	+	"Seed for sprng library should contain at least 9 digits\n"
926	+	"OOPSE will generate a seed for user\n");
927	+	painCave.isFatal = 0;
928	+	simError();
929	+
930	+	//using seed generated by system instead of invalid seed set by user
931	+	#ifndef IS_MPI
932	+	seedValue = make_sprng_seed();
933	+	#else
934	+	if (worldRank == 0){
935	+	seedValue = make_sprng_seed();
936	+	}
937	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
938	+	#endif
939	+	}
940	+	}//end of if branch of globals->haveSeed()
941	+	else{
942	+
943	+	#ifndef IS_MPI
944	+	seedValue = make_sprng_seed();
945	+	#else
946	+	if (worldRank == 0){
947	+	seedValue = make_sprng_seed();
948	+	}
949	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
950	+	#endif
951	+	}//end of globals->haveSeed()
952	+
953	+	for (int i = 0; i < nInfo; i++){
954	+	info[i].setSeed(seedValue);
955	+	}
956	+
957	+	#ifdef IS_MPI
958	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959	+	MPIcheckPoint();
960	+	#endif // is_mpi
961	+	}
962	+
963	+
964	+	void SimSetup::finalInfoCheck(void){
965	+	int index;
966	+	int usesDipoles;
967	+	int usesCharges;
968	+	int i;
969	+
970	+	for (i = 0; i < nInfo; i++){
971	+	// check electrostatic parameters
972	+
973	+	index = 0;
974	+	usesDipoles = 0;
975	+	while ((index < info[i].n_atoms) && !usesDipoles){
976	+	usesDipoles = (info[i].atoms[index])->hasDipole();
977	+	index++;
978	+	}
979	+	index = 0;
980	+	usesCharges = 0;
981	+	while ((index < info[i].n_atoms) && !usesCharges){
982	+	usesCharges= (info[i].atoms[index])->hasCharge();
983	+	index++;
984	+	}
985	+	#ifdef IS_MPI
986	+	int myUse = usesDipoles;
987	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988	+	#endif //is_mpi
989	+
990	+	double theEcr, theEst;
991	+
992	+	if (globals->getUseRF()){
993	+	info[i].useReactionField = 1;
994	+
995	+	if (!globals->haveECR()){
996	+	sprintf(painCave.errMsg,
997	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
998	+	"\tOOPSE will use a default value of 15.0 angstroms"
999	+	"\tfor the electrostaticCutoffRadius.\n");
1000	+	painCave.isFatal = 0;
1001	+	simError();
1002	+	theEcr = 15.0;
1003	+	}
1004	+	else{
1005	+	theEcr = globals->getECR();
1006	+	}
1007	+
1008	+	if (!globals->haveEST()){
1009	+	sprintf(painCave.errMsg,
1010	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1011	+	"\tOOPSE will use a default value of\n"
1012	+	"\t0.05 * electrostaticCutoffRadius\n"
1013	+	"\tfor the electrostaticSkinThickness\n");
1014	+	painCave.isFatal = 0;
1015	+	simError();
1016	+	theEst = 0.05 * theEcr;
1017	+	}
1018	+	else{
1019	+	theEst = globals->getEST();
1020	+	}
1021	+
1022	+	info[i].setDefaultEcr(theEcr, theEst);
1023	+
1024	+	if (!globals->haveDielectric()){
1025	+	sprintf(painCave.errMsg,
1026	+	"SimSetup Error: No Dielectric constant was set.\n"
1027	+	"\tYou are trying to use Reaction Field without"
1028	+	"\tsetting a dielectric constant!\n");
1029	+	painCave.isFatal = 1;
1030	+	simError();
1031	+	}
1032	+	info[i].dielectric = globals->getDielectric();
1033	+	}
1034	+	else{
1035	+	if (usesDipoles || usesCharges){
1036	+	if (!globals->haveECR()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1039	+	"\tOOPSE will use a default value of 15.0 angstroms"
1040	+	"\tfor the electrostaticCutoffRadius.\n");
1041	+	painCave.isFatal = 0;
1042	+	simError();
1043	+	theEcr = 15.0;
1044	+	}
1045	+	else{
1046	+	theEcr = globals->getECR();
1047	+	}
1048	+
1049	+	if (!globals->haveEST()){
1050	+	sprintf(painCave.errMsg,
1051	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1052	+	"\tOOPSE will use a default value of\n"
1053	+	"\t0.05 * electrostaticCutoffRadius\n"
1054	+	"\tfor the electrostaticSkinThickness\n");
1055	+	painCave.isFatal = 0;
1056	+	simError();
1057	+	theEst = 0.05 * theEcr;
1058	+	}
1059	+	else{
1060	+	theEst = globals->getEST();
1061	+	}
1062	+
1063	+	info[i].setDefaultEcr(theEcr, theEst);
1064	+	}
1065	+	}
1066	+	}
1067	+	#ifdef IS_MPI
1068	+	strcpy(checkPointMsg, "post processing checks out");
1069	+	MPIcheckPoint();
1070	+	#endif // is_mpi
1071	+	}
1072	+
1073	+	void SimSetup::initSystemCoords(void){
1074	+	int i;
1075	+
1076	+	char* inName;
1077	+
1078	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079	+
1080	+	for (i = 0; i < info[0].n_atoms; i++)
1081	+	info[0].atoms[i]->setCoords();
1082	+
1083	+	if (globals->haveInitialConfig()){
1084	+	InitializeFromFile* fileInit;
1085	+	#ifdef IS_MPI // is_mpi
1086	+	if (worldRank == 0){
1087	+	#endif //is_mpi
1088	+	inName = globals->getInitialConfig();
1089	+	fileInit = new InitializeFromFile(inName);
1090	+	#ifdef IS_MPI
1091	+	}
1092	+	else
1093	+	fileInit = new InitializeFromFile(NULL);
1094	+	#endif
1095	+	fileInit->readInit(info); // default velocities on
1096	+
1097	+	delete fileInit;
1098	+	}
1099	+	else{
1100	+
1101	+	// no init from bass
1102	+
1103	+	sprintf(painCave.errMsg,
1104	+	"Cannot intialize a simulation without an initial configuration file.\n");
1105	+	painCave.isFatal = 1;;
1106	+	simError();
1107	+
1108	+	}
1109	+
1110	+	#ifdef IS_MPI
1111	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112	+	MPIcheckPoint();
1113	+	#endif // is_mpi
1114	+	}
1115
1152	–	if( current_comp_mol >= components_nmol[current_comp] ){
1116
1117	<	current_comp_mol = 0;
1118	<	current_comp++;
1117	>	void SimSetup::makeOutNames(void){
1118	>	int k;
1119	>
1120	>
1121	>	for (k = 0; k < nInfo; k++){
1122	>	#ifdef IS_MPI
1123	>	if (worldRank == 0){
1124	>	#endif // is_mpi
1125	>
1126	>	if (globals->haveFinalConfig()){
1127	>	strcpy(info[k].finalName, globals->getFinalConfig());
1128	>	}
1129	>	else{
1130	>	strcpy(info[k].finalName, inFileName);
1131	>	char* endTest;
1132	>	int nameLength = strlen(info[k].finalName);
1133	>	endTest = &(info[k].finalName[nameLength - 5]);
1134	>	if (!strcmp(endTest, ".bass")){
1135	>	strcpy(endTest, ".eor");
1136	>	}
1137	>	else if (!strcmp(endTest, ".BASS")){
1138	>	strcpy(endTest, ".eor");
1139	>	}
1140	>	else{
1141	>	endTest = &(info[k].finalName[nameLength - 4]);
1142	>	if (!strcmp(endTest, ".bss")){
1143	>	strcpy(endTest, ".eor");
1144	>	}
1145	>	else if (!strcmp(endTest, ".mdl")){
1146	>	strcpy(endTest, ".eor");
1147	>	}
1148	>	else{
1149	>	strcat(info[k].finalName, ".eor");
1150	>	}
1151	>	}
1152	>	}
1153	>
1154	>	// make the sample and status out names
1155	>
1156	>	strcpy(info[k].sampleName, inFileName);
1157	>	char* endTest;
1158	>	int nameLength = strlen(info[k].sampleName);
1159	>	endTest = &(info[k].sampleName[nameLength - 5]);
1160	>	if (!strcmp(endTest, ".bass")){
1161	>	strcpy(endTest, ".dump");
1162	>	}
1163	>	else if (!strcmp(endTest, ".BASS")){
1164	>	strcpy(endTest, ".dump");
1165	>	}
1166	>	else{
1167	>	endTest = &(info[k].sampleName[nameLength - 4]);
1168	>	if (!strcmp(endTest, ".bss")){
1169	>	strcpy(endTest, ".dump");
1170	>	}
1171	>	else if (!strcmp(endTest, ".mdl")){
1172	>	strcpy(endTest, ".dump");
1173	>	}
1174	>	else{
1175	>	strcat(info[k].sampleName, ".dump");
1176	>	}
1177	>	}
1178	>
1179	>	strcpy(info[k].statusName, inFileName);
1180	>	nameLength = strlen(info[k].statusName);
1181	>	endTest = &(info[k].statusName[nameLength - 5]);
1182	>	if (!strcmp(endTest, ".bass")){
1183	>	strcpy(endTest, ".stat");
1184	>	}
1185	>	else if (!strcmp(endTest, ".BASS")){
1186	>	strcpy(endTest, ".stat");
1187	>	}
1188	>	else{
1189	>	endTest = &(info[k].statusName[nameLength - 4]);
1190	>	if (!strcmp(endTest, ".bss")){
1191	>	strcpy(endTest, ".stat");
1192	>	}
1193	>	else if (!strcmp(endTest, ".mdl")){
1194	>	strcpy(endTest, ".stat");
1195	>	}
1196	>	else{
1197	>	strcat(info[k].statusName, ".stat");
1198	>	}
1199	>	}
1200	>
1201	>	#ifdef IS_MPI
1202	>
1203	>	}
1204	>	#endif // is_mpi
1205	>	}
1206	>	}
1207	>
1208	>
1209	>	void SimSetup::sysObjectsCreation(void){
1210	>	int i, k;
1211	>
1212	>	// create the forceField
1213	>
1214	>	createFF();
1215	>
1216	>	// extract componentList
1217	>
1218	>	compList();
1219	>
1220	>	// calc the number of atoms, bond, bends, and torsions
1221	>
1222	>	calcSysValues();
1223	>
1224	>	#ifdef IS_MPI
1225	>	// divide the molecules among the processors
1226	>
1227	>	mpiMolDivide();
1228	>	#endif //is_mpi
1229	>
1230	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231	>
1232	>	makeSysArrays();
1233	>
1234	>	// make and initialize the molecules (all but atomic coordinates)
1235	>
1236	>	makeMolecules();
1237	>
1238	>	for (k = 0; k < nInfo; k++){
1239	>	info[k].identArray = new int[info[k].n_atoms];
1240	>	for (i = 0; i < info[k].n_atoms; i++){
1241	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1242	>	}
1243	>	}
1244	>	}
1245	>
1246	>
1247	>	void SimSetup::createFF(void){
1248	>	switch (ffCase){
1249	>	case FF_DUFF:
1250	>	the_ff = new DUFF();
1251	>	break;
1252	>
1253	>	case FF_LJ:
1254	>	the_ff = new LJFF();
1255	>	break;
1256	>
1257	>	case FF_EAM:
1258	>	the_ff = new EAM_FF();
1259	>	break;
1260	>
1261	>	case FF_H2O:
1262	>	the_ff = new WATER();
1263	>	break;
1264	>
1265	>	default:
1266	>	sprintf(painCave.errMsg,
1267	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1268	>	painCave.isFatal = 1;
1269	>	simError();
1270	>	}
1271	>
1272	>	#ifdef IS_MPI
1273	>	strcpy(checkPointMsg, "ForceField creation successful");
1274	>	MPIcheckPoint();
1275	>	#endif // is_mpi
1276	>	}
1277	>
1278	>
1279	>	void SimSetup::compList(void){
1280	>	int i;
1281	>	char* id;
1282	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1283	>	LinkedMolStamp* currentStamp = NULL;
1284	>	comp_stamps = new MoleculeStamp * [n_components];
1285	>
1286	>	// make an array of molecule stamps that match the components used.
1287	>	// also extract the used stamps out into a separate linked list
1288	>
1289	>	for (i = 0; i < nInfo; i++){
1290	>	info[i].nComponents = n_components;
1291	>	info[i].componentsNmol = components_nmol;
1292	>	info[i].compStamps = comp_stamps;
1293	>	info[i].headStamp = headStamp;
1294	>	}
1295	>
1296	>
1297	>	for (i = 0; i < n_components; i++){
1298	>	id = the_components[i]->getType();
1299	>	comp_stamps[i] = NULL;
1300	>
1301	>	// check to make sure the component isn't already in the list
1302	>
1303	>	comp_stamps[i] = headStamp->match(id);
1304	>	if (comp_stamps[i] == NULL){
1305	>	// extract the component from the list;
1306	>
1307	>	currentStamp = stamps->extractMolStamp(id);
1308	>	if (currentStamp == NULL){
1309	>	sprintf(painCave.errMsg,
1310	>	"SimSetup error: Component \"%s\" was not found in the "
1311	>	"list of declared molecules\n",
1312	>	id);
1313	>	painCave.isFatal = 1;
1314	>	simError();
1315	>	}
1316	>
1317	>	headStamp->add(currentStamp);
1318	>	comp_stamps[i] = headStamp->match(id);
1319	>	}
1320	>	}
1321	>
1322	>	#ifdef IS_MPI
1323	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1324	>	MPIcheckPoint();
1325	>	#endif // is_mpi
1326	>	}
1327	>
1328	>	void SimSetup::calcSysValues(void){
1329	>	int i;
1330	>
1331	>	int* molMembershipArray;
1332	>
1333	>	tot_atoms = 0;
1334	>	tot_bonds = 0;
1335	>	tot_bends = 0;
1336	>	tot_torsions = 0;
1337	>	tot_rigid = 0;
1338	>	for (i = 0; i < n_components; i++){
1339	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344	>	}
1345	>
1346	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347	>	molMembershipArray = new int[tot_atoms];
1348	>
1349	>	for (i = 0; i < nInfo; i++){
1350	>	info[i].n_atoms = tot_atoms;
1351	>	info[i].n_bonds = tot_bonds;
1352	>	info[i].n_bends = tot_bends;
1353	>	info[i].n_torsions = tot_torsions;
1354	>	info[i].n_SRI = tot_SRI;
1355	>	info[i].n_mol = tot_nmol;
1356	>
1357	>	info[i].molMembershipArray = molMembershipArray;
1358	>	}
1359	>	}
1360	>
1361	>	#ifdef IS_MPI
1362	>
1363	>	void SimSetup::mpiMolDivide(void){
1364	>	int i, j, k;
1365	>	int localMol, allMol;
1366	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	>	int local_rigid;
1368	>	vector<int> globalAtomIndex;
1369	>	vector<int> globalMolIndex;
1370	>
1371	>	mpiSim = new mpiSimulation(info);
1372	>
1373	>	mpiSim->divideLabor();
1374	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1375	>	globalMolIndex = mpiSim->getGlobalMolIndex();
1376	>
1377	>	// set up the local variables
1378	>
1379	>	mol2proc = mpiSim->getMolToProcMap();
1380	>	molCompType = mpiSim->getMolComponentType();
1381	>
1382	>	allMol = 0;
1383	>	localMol = 0;
1384	>	local_atoms = 0;
1385	>	local_bonds = 0;
1386	>	local_bends = 0;
1387	>	local_torsions = 0;
1388	>	local_rigid = 0;
1389	>	globalAtomCounter = 0;
1390	>
1391	>	for (i = 0; i < n_components; i++){
1392	>	for (j = 0; j < components_nmol[i]; j++){
1393	>	if (mol2proc[allMol] == worldRank){
1394	>	local_atoms += comp_stamps[i]->getNAtoms();
1395	>	local_bonds += comp_stamps[i]->getNBonds();
1396	>	local_bends += comp_stamps[i]->getNBends();
1397	>	local_torsions += comp_stamps[i]->getNTorsions();
1398	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1399	>	localMol++;
1400	>	}
1401	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1402	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1403	>	globalAtomCounter++;
1404	>	}
1405	>
1406	>	allMol++;
1407	>	}
1408	>	}
1409	>	local_SRI = local_bonds + local_bends + local_torsions;
1410	>
1411	>	info[0].n_atoms = mpiSim->getMyNlocal();
1412	>
1413	>
1414	>	if (local_atoms != info[0].n_atoms){
1415	>	sprintf(painCave.errMsg,
1416	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1417	>	"\tlocalAtom (%d) are not equal.\n",
1418	>	info[0].n_atoms, local_atoms);
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422	>
1423	>	info[0].n_bonds = local_bonds;
1424	>	info[0].n_bends = local_bends;
1425	>	info[0].n_torsions = local_torsions;
1426	>	info[0].n_SRI = local_SRI;
1427	>	info[0].n_mol = localMol;
1428	>
1429	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1430	>	MPIcheckPoint();
1431	>	}
1432	>
1433	>	#endif // is_mpi
1434	>
1435	>
1436	>	void SimSetup::makeSysArrays(void){
1437	>
1438	>	#ifndef IS_MPI
1439	>	int k, j;
1440	>	#endif // is_mpi
1441	>	int i, l;
1442	>
1443	>	Atom** the_atoms;
1444	>	Molecule* the_molecules;
1445	>
1446	>	for (l = 0; l < nInfo; l++){
1447	>	// create the atom and short range interaction arrays
1448	>
1449	>	the_atoms = new Atom * [info[l].n_atoms];
1450	>	the_molecules = new Molecule[info[l].n_mol];
1451	>	int molIndex;
1452	>
1453	>	// initialize the molecule's stampID's
1454	>
1455	>	#ifdef IS_MPI
1456	>
1457	>
1458	>	molIndex = 0;
1459	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1460	>	if (mol2proc[i] == worldRank){
1461	>	the_molecules[molIndex].setStampID(molCompType[i]);
1462	>	the_molecules[molIndex].setMyIndex(molIndex);
1463	>	the_molecules[molIndex].setGlobalIndex(i);
1464	>	molIndex++;
1465	>	}
1466	>	}
1467	>
1468	>	#else // is_mpi
1469	>
1470	>	molIndex = 0;
1471	>	globalAtomCounter = 0;
1472	>	for (i = 0; i < n_components; i++){
1473	>	for (j = 0; j < components_nmol[i]; j++){
1474	>	the_molecules[molIndex].setStampID(i);
1475	>	the_molecules[molIndex].setMyIndex(molIndex);
1476	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1477	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1478	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1479	>	globalAtomCounter++;
1480	>	}
1481	>	molIndex++;
1482	>	}
1483	>	}
1484	>
1485	>
1486	>	#endif // is_mpi
1487	>
1488	>	info[l].globalExcludes = new int;
1489	>	info[l].globalExcludes[0] = 0;
1490	>
1491	>	// set the arrays into the SimInfo object
1492	>
1493	>	info[l].atoms = the_atoms;
1494	>	info[l].molecules = the_molecules;
1495	>	info[l].nGlobalExcludes = 0;
1496	>
1497	>	the_ff->setSimInfo(info);
1498	>	}
1499	>	}
1500	>
1501	>	void SimSetup::makeIntegrator(void){
1502	>	int k;
1503	>
1504	>	NVE<RealIntegrator>* myNVE = NULL;
1505	>	NVT<RealIntegrator>* myNVT = NULL;
1506	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1507	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1508	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1509	>
1510	>	for (k = 0; k < nInfo; k++){
1511	>	switch (ensembleCase){
1512	>	case NVE_ENS:
1513	>	if (globals->haveZconstraints()){
1514	>	setupZConstraint(info[k]);
1515	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1516	>	}
1517	>	else{
1518	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1519	>	}
1520	>
1521	>	info->the_integrator = myNVE;
1522	>	break;
1523	>
1524	>	case NVT_ENS:
1525	>	if (globals->haveZconstraints()){
1526	>	setupZConstraint(info[k]);
1527	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1528	>	}
1529	>	else
1530	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1531	>
1532	>	myNVT->setTargetTemp(globals->getTargetTemp());
1533	>
1534	>	if (globals->haveTauThermostat())
1535	>	myNVT->setTauThermostat(globals->getTauThermostat());
1536	>	else{
1537	>	sprintf(painCave.errMsg,
1538	>	"SimSetup error: If you use the NVT\n"
1539	>	"\tensemble, you must set tauThermostat.\n");
1540	>	painCave.isFatal = 1;
1541	>	simError();
1542	>	}
1543	>
1544	>	info->the_integrator = myNVT;
1545	>	break;
1546	>
1547	>	case NPTi_ENS:
1548	>	if (globals->haveZconstraints()){
1549	>	setupZConstraint(info[k]);
1550	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1551	>	}
1552	>	else
1553	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1554	>
1555	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1556	>
1557	>	if (globals->haveTargetPressure())
1558	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1559	>	else{
1560	>	sprintf(painCave.errMsg,
1561	>	"SimSetup error: If you use a constant pressure\n"
1562	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566	>
1567	>	if (globals->haveTauThermostat())
1568	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1569	>	else{
1570	>	sprintf(painCave.errMsg,
1571	>	"SimSetup error: If you use an NPT\n"
1572	>	"\tensemble, you must set tauThermostat.\n");
1573	>	painCave.isFatal = 1;
1574	>	simError();
1575	>	}
1576	>
1577	>	if (globals->haveTauBarostat())
1578	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1579	>	else{
1580	>	sprintf(painCave.errMsg,
1581	>	"SimSetup error: If you use an NPT\n"
1582	>	"\tensemble, you must set tauBarostat.\n");
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585	>	}
1586	>
1587	>	info->the_integrator = myNPTi;
1588	>	break;
1589	>
1590	>	case NPTf_ENS:
1591	>	if (globals->haveZconstraints()){
1592	>	setupZConstraint(info[k]);
1593	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1594	>	}
1595	>	else
1596	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1597	>
1598	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1599	>
1600	>	if (globals->haveTargetPressure())
1601	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1602	>	else{
1603	>	sprintf(painCave.errMsg,
1604	>	"SimSetup error: If you use a constant pressure\n"
1605	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1606	>	painCave.isFatal = 1;
1607	>	simError();
1608	>	}
1609	>
1610	>	if (globals->haveTauThermostat())
1611	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1612	>
1613	>	else{
1614	>	sprintf(painCave.errMsg,
1615	>	"SimSetup error: If you use an NPT\n"
1616	>	"\tensemble, you must set tauThermostat.\n");
1617	>	painCave.isFatal = 1;
1618	>	simError();
1619	>	}
1620	>
1621	>	if (globals->haveTauBarostat())
1622	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1623	>
1624	>	else{
1625	>	sprintf(painCave.errMsg,
1626	>	"SimSetup error: If you use an NPT\n"
1627	>	"\tensemble, you must set tauBarostat.\n");
1628	>	painCave.isFatal = 1;
1629	>	simError();
1630	>	}
1631	>
1632	>	info->the_integrator = myNPTf;
1633	>	break;
1634	>
1635	>	case NPTxyz_ENS:
1636	>	if (globals->haveZconstraints()){
1637	>	setupZConstraint(info[k]);
1638	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1639	>	}
1640	>	else
1641	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1642	>
1643	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1644	>
1645	>	if (globals->haveTargetPressure())
1646	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1647	>	else{
1648	>	sprintf(painCave.errMsg,
1649	>	"SimSetup error: If you use a constant pressure\n"
1650	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1651	>	painCave.isFatal = 1;
1652	>	simError();
1653	>	}
1654	>
1655	>	if (globals->haveTauThermostat())
1656	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1657	>	else{
1658	>	sprintf(painCave.errMsg,
1659	>	"SimSetup error: If you use an NPT\n"
1660	>	"\tensemble, you must set tauThermostat.\n");
1661	>	painCave.isFatal = 1;
1662	>	simError();
1663	>	}
1664	>
1665	>	if (globals->haveTauBarostat())
1666	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1667	>	else{
1668	>	sprintf(painCave.errMsg,
1669	>	"SimSetup error: If you use an NPT\n"
1670	>	"\tensemble, you must set tauBarostat.\n");
1671	>	painCave.isFatal = 1;
1672	>	simError();
1673	>	}
1674	>
1675	>	info->the_integrator = myNPTxyz;
1676	>	break;
1677	>
1678	>	default:
1679	>	sprintf(painCave.errMsg,
1680	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1681	>	painCave.isFatal = 1;
1682	>	simError();
1683	>	}
1684		}
1685		}
1686	+
1687	+	void SimSetup::initFortran(void){
1688	+	info[0].refreshSim();
1689	+
1690	+	if (!strcmp(info[0].mixingRule, "standard")){
1691	+	the_ff->initForceField(LB_MIXING_RULE);
1692	+	}
1693	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1694	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1695	+	}
1696	+	else{
1697	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1698	+	info[0].mixingRule);
1699	+	painCave.isFatal = 1;
1700	+	simError();
1701	+	}
1702	+
1703	+
1704	+	#ifdef IS_MPI
1705	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1706	+	MPIcheckPoint();
1707	+	#endif // is_mpi
1708	+	}
1709	+
1710	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1711	+	int nZConstraints;
1712	+	ZconStamp** zconStamp;
1713	+
1714	+	if (globals->haveZconstraintTime()){
1715	+	//add sample time of z-constraint  into SimInfo's property list
1716	+	DoubleData* zconsTimeProp = new DoubleData();
1717	+	zconsTimeProp->setID(ZCONSTIME_ID);
1718	+	zconsTimeProp->setData(globals->getZconsTime());
1719	+	theInfo.addProperty(zconsTimeProp);
1720	+	}
1721	+	else{
1722	+	sprintf(painCave.errMsg,
1723	+	"ZConstraint error: If you use a ZConstraint,\n"
1724	+	"\tyou must set zconsTime.\n");
1725	+	painCave.isFatal = 1;
1726	+	simError();
1727	+	}
1728	+
1729	+	//push zconsTol into siminfo, if user does not specify
1730	+	//value for zconsTol, a default value will be used
1731	+	DoubleData* zconsTol = new DoubleData();
1732	+	zconsTol->setID(ZCONSTOL_ID);
1733	+	if (globals->haveZconsTol()){
1734	+	zconsTol->setData(globals->getZconsTol());
1735	+	}
1736	+	else{
1737	+	double defaultZConsTol = 0.01;
1738	+	sprintf(painCave.errMsg,
1739	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1740	+	"\tOOPSE will use a default value of %f.\n"
1741	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1742	+	defaultZConsTol);
1743	+	painCave.isFatal = 0;
1744	+	simError();
1745	+
1746	+	zconsTol->setData(defaultZConsTol);
1747	+	}
1748	+	theInfo.addProperty(zconsTol);
1749	+
1750	+	//set Force Subtraction Policy
1751	+	StringData* zconsForcePolicy = new StringData();
1752	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1753	+
1754	+	if (globals->haveZconsForcePolicy()){
1755	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1756	+	}
1757	+	else{
1758	+	sprintf(painCave.errMsg,
1759	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1760	+	"\tOOPSE will use PolicyByMass.\n"
1761	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1762	+	painCave.isFatal = 0;
1763	+	simError();
1764	+	zconsForcePolicy->setData("BYMASS");
1765	+	}
1766	+
1767	+	theInfo.addProperty(zconsForcePolicy);
1768	+
1769	+	//set zcons gap
1770	+	DoubleData* zconsGap = new DoubleData();
1771	+	zconsGap->setID(ZCONSGAP_ID);
1772	+
1773	+	if (globals->haveZConsGap()){
1774	+	zconsGap->setData(globals->getZconsGap());
1775	+	theInfo.addProperty(zconsGap);
1776	+	}
1777	+
1778	+	//set zcons fixtime
1779	+	DoubleData* zconsFixtime = new DoubleData();
1780	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1781	+
1782	+	if (globals->haveZConsFixTime()){
1783	+	zconsFixtime->setData(globals->getZconsFixtime());
1784	+	theInfo.addProperty(zconsFixtime);
1785	+	}
1786	+
1787	+	//set zconsUsingSMD
1788	+	IntData* zconsUsingSMD = new IntData();
1789	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1790	+
1791	+	if (globals->haveZConsUsingSMD()){
1792	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1793	+	theInfo.addProperty(zconsUsingSMD);
1794	+	}
1795	+
1796	+	//Determine the name of ouput file and add it into SimInfo's property list
1797	+	//Be careful, do not use inFileName, since it is a pointer which
1798	+	//point to a string at master node, and slave nodes do not contain that string
1799	+
1800	+	string zconsOutput(theInfo.finalName);
1801	+
1802	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1803	+
1804	+	StringData* zconsFilename = new StringData();
1805	+	zconsFilename->setID(ZCONSFILENAME_ID);
1806	+	zconsFilename->setData(zconsOutput);
1807	+
1808	+	theInfo.addProperty(zconsFilename);
1809	+
1810	+	//setup index, pos and other parameters of z-constraint molecules
1811	+	nZConstraints = globals->getNzConstraints();
1812	+	theInfo.nZconstraints = nZConstraints;
1813	+
1814	+	zconStamp = globals->getZconStamp();
1815	+	ZConsParaItem tempParaItem;
1816	+
1817	+	ZConsParaData* zconsParaData = new ZConsParaData();
1818	+	zconsParaData->setID(ZCONSPARADATA_ID);
1819	+
1820	+	for (int i = 0; i < nZConstraints; i++){
1821	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1822	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1823	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1824	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1825	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1826	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1827	+	zconsParaData->addItem(tempParaItem);
1828	+	}
1829	+
1830	+	//check the uniqueness of index
1831	+	if(!zconsParaData->isIndexUnique()){
1832	+	sprintf(painCave.errMsg,
1833	+	"ZConstraint Error: molIndex is not unique!\n");
1834	+	painCave.isFatal = 1;
1835	+	simError();
1836	+	}
1837	+
1838	+	//sort the parameters by index of molecules
1839	+	zconsParaData->sortByIndex();
1840	+
1841	+	//push data into siminfo, therefore, we can retrieve later
1842	+	theInfo.addProperty(zconsParaData);
1843	+	}
1844	+
1845	+	void SimSetup::makeMinimizer(){
1846	+
1847	+	OOPSEMinimizer* myOOPSEMinimizer;
1848	+	MinimizerParameterSet* param;
1849	+	char minimizerName[100];
1850	+
1851	+	for (int i = 0; i < nInfo; i++){
1852	+
1853	+	//prepare parameter set for minimizer
1854	+	param = new MinimizerParameterSet();
1855	+	param->setDefaultParameter();
1856	+
1857	+	if (globals->haveMinimizer()){
1858	+	param->setFTol(globals->getMinFTol());
1859	+	}
1860	+
1861	+	if (globals->haveMinGTol()){
1862	+	param->setGTol(globals->getMinGTol());
1863	+	}
1864	+
1865	+	if (globals->haveMinMaxIter()){
1866	+	param->setMaxIteration(globals->getMinMaxIter());
1867	+	}
1868	+
1869	+	if (globals->haveMinWriteFrq()){
1870	+	param->setMaxIteration(globals->getMinMaxIter());
1871	+	}
1872	+
1873	+	if (globals->haveMinWriteFrq()){
1874	+	param->setWriteFrq(globals->getMinWriteFrq());
1875	+	}
1876	+
1877	+	if (globals->haveMinStepSize()){
1878	+	param->setStepSize(globals->getMinStepSize());
1879	+	}
1880	+
1881	+	if (globals->haveMinLSMaxIter()){
1882	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1883	+	}
1884	+
1885	+	if (globals->haveMinLSTol()){
1886	+	param->setLineSearchTol(globals->getMinLSTol());
1887	+	}
1888	+
1889	+	strcpy(minimizerName, globals->getMinimizer());
1890	+
1891	+	if (!strcasecmp(minimizerName, "CG")){
1892	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1893	+	}
1894	+	else if (!strcasecmp(minimizerName, "SD")){
1895	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1896	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1897	+	}
1898	+	else{
1899	+	sprintf(painCave.errMsg,
1900	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1901	+	painCave.isFatal = 0;
1902	+	simError();
1903	+
1904	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1905	+	}
1906	+	info[i].the_integrator = myOOPSEMinimizer;
1907	+
1908	+	//store the minimizer into simInfo
1909	+	info[i].the_minimizer = myOOPSEMinimizer;
1910	+	info[i].has_minimizer = true;
1911	+	}
1912	+
1913	+	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines