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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 670 by mmeineke, Thu Aug 7 21:47:18 2003 UTC vs.
Revision 1032 by tim, Fri Feb 6 19:05:07 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
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 "ConjugateMinimizer.hpp"
13
14		#ifdef IS_MPI
15		#include "mpiBASS.h"
#	Line 20 | Line 22
22		#define NVT_ENS        1
23		#define NPTi_ENS       2
24		#define NPTf_ENS       3
25	<	#define NPTim_ENS      4
24	<	#define NPTfm_ENS      5
25	<	#define NVEZCONS_ENS   6
26	<	#define NVTZCONS_ENS   7
27	<	#define NPTiZCONS_ENS  8
28	<	#define NPTfZCONS_ENS  9
29	<	#define NPTimZCONS_ENS 10
30	<	#define NPTfmZCONS_ENS 11
25	>	#define NPTxyz_ENS     4
26
32	–	#define FF_DUFF 0
33	–	#define FF_LJ   1
34	–	#define FF_EAM  2
27
28	+	#define FF_DUFF  0
29	+	#define FF_LJ    1
30	+	#define FF_EAM   2
31	+	#define FF_H2O 3
32	+
33		using namespace std;
34
35	+	/**
36	+	* Check whether dividend is divisble by divisor or not
37	+	*/
38	+	bool isDivisible(double dividend, double divisor){
39	+	double tolerance = 0.000001;
40	+	double quotient;
41	+	double diff;
42	+	int intQuotient;
43	+
44	+	quotient = dividend / divisor;
45	+
46	+	if (quotient < 0)
47	+	quotient = -quotient;
48	+
49	+	intQuotient = int (quotient + tolerance);
50	+
51	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
52	+
53	+	if (diff <= tolerance)
54	+	return true;
55	+	else
56	+	return false;
57	+	}
58	+
59		SimSetup::SimSetup(){
60
61	+	initSuspend = false;
62		isInfoArray = 0;
63		nInfo = 1;
64	<
64	>
65		stamps = new MakeStamps();
66		globals = new Globals();
67	<
68	<
67	>
68	>
69		#ifdef IS_MPI
70	<	strcpy( checkPointMsg, "SimSetup creation successful" );
70	>	strcpy(checkPointMsg, "SimSetup creation successful");
71		MPIcheckPoint();
72		#endif // IS_MPI
73		}
#	Line 55 | Line 77 | SimSetup::~SimSetup(){
77		delete globals;
78		}
79
80	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
81	<	info = the_info;
82	<	nInfo = theNinfo;
83	<	isInfoArray = 1;
80	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
81	>	info = the_info;
82	>	nInfo = theNinfo;
83	>	isInfoArray = 1;
84	>	initSuspend = true;
85		}
86
87
88	<	void SimSetup::parseFile( char* fileName ){
66	<
88	>	void SimSetup::parseFile(char* fileName){
89		#ifdef IS_MPI
90	<	if( worldRank == 0 ){
90	>	if (worldRank == 0){
91		#endif // is_mpi
92	<
92	>
93		inFileName = fileName;
94	<	set_interface_stamps( stamps, globals );
95	<
94	>	set_interface_stamps(stamps, globals);
95	>
96		#ifdef IS_MPI
97		mpiEventInit();
98		#endif
99
100	<	yacc_BASS( fileName );
100	>	yacc_BASS(fileName);
101
102		#ifdef IS_MPI
103		throwMPIEvent(NULL);
104		}
105	<	else receiveParse();
105	>	else{
106	>	receiveParse();
107	>	}
108		#endif
109
110		}
111
112		#ifdef IS_MPI
113		void SimSetup::receiveParse(void){
114	<
115	<	set_interface_stamps( stamps, globals );
116	<	mpiEventInit();
117	<	MPIcheckPoint();
94	<	mpiEventLoop();
95	<
114	>	set_interface_stamps(stamps, globals);
115	>	mpiEventInit();
116	>	MPIcheckPoint();
117	>	mpiEventLoop();
118		}
119
120		#endif // is_mpi
121
122		void SimSetup::createSim(void){
123
102	–	int i, j, k, globalAtomIndex;
103	–
124		// gather all of the information from the Bass file
125	<
125	>
126		gatherInfo();
127
128		// creation of complex system objects
#	Line 110 | Line 130 | void SimSetup::createSim(void){
130		sysObjectsCreation();
131
132		// check on the post processing info
133	<
133	>
134		finalInfoCheck();
135
136		// initialize the system coordinates
137
138	<	if( !isInfoArray ) initSystemCoords();
138	>	if ( !initSuspend ){
139	>	initSystemCoords();
140
141	+	if( !(globals->getUseInitTime()) )
142	+	info[0].currentTime = 0.0;
143	+	}
144	+
145		// make the output filenames
146
147		makeOutNames();
148	<
149	<	// make the integrator
148	>
149	>	if (globals->haveMinimizer())
150	>	// make minimizer
151	>	makeMinimizer();
152	>	else
153	>	// make the integrator
154	>	makeIntegrator();
155
126	–	makeIntegrator();
127	–
156		#ifdef IS_MPI
157		mpiSim->mpiRefresh();
158		#endif
#	Line 132 | Line 160 | void SimSetup::createSim(void){
160		// initialize the Fortran
161
162		initFortran();
135	–
136	–
137	–
163		}
164
165
166	<	void SimSetup::makeMolecules( void ){
167	<
143	<	int k,l;
166	>	void SimSetup::makeMolecules(void){
167	>	int k;
168		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169		molInit molInfo;
170		DirectionalAtom* dAtom;
#	Line 155 | Line 179 | void SimSetup::makeMolecules( void ){
179		bend_set* theBends;
180		torsion_set* theTorsions;
181
158	–
182		//init the forceField paramters
183
184		the_ff->readParams();
185
186	<
186	>
187		// init the atoms
188
189	+	double phi, theta, psi;
190	+	double sux, suy, suz;
191	+	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
192		double ux, uy, uz, u, uSqr;
167	–
168	–	for(k=0; k<nInfo; k++){
169	–
170	–	the_ff->setSimInfo( &(info[k]) );
193
194	+	for (k = 0; k < nInfo; k++){
195	+	the_ff->setSimInfo(&(info[k]));
196	+
197		atomOffset = 0;
198		excludeOffset = 0;
199	<	for(i=0; i<info[k].n_mol; i++){
175	<
199	>	for (i = 0; i < info[k].n_mol; i++){
200		stampID = info[k].molecules[i].getStampID();
201
202	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
203	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
204	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
202	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
203	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
204	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
205		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
206		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
207	<
207	>
208		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
209		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
210	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
211	<	molInfo.myBends = new Bend*[molInfo.nBends];
212	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
210	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
211	>	molInfo.myBends = new Bend * [molInfo.nBends];
212	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
213
214		theBonds = new bond_pair[molInfo.nBonds];
215		theBends = new bend_set[molInfo.nBends];
216		theTorsions = new torsion_set[molInfo.nTorsions];
217	<
217	>
218		// make the Atoms
219	<
220	<	for(j=0; j<molInfo.nAtoms; j++){
221	<
222	<	currentAtom = comp_stamps[stampID]->getAtom( j );
223	<	if( currentAtom->haveOrientation() ){
224	<
225	<	dAtom = new DirectionalAtom( (j + atomOffset),
226	<	info[k].getConfiguration() );
227	<	info[k].n_oriented++;
228	<	molInfo.myAtoms[j] = dAtom;
229	<
230	<	ux = currentAtom->getOrntX();
231	<	uy = currentAtom->getOrntY();
232	<	uz = currentAtom->getOrntZ();
233	<
234	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
235	<
236	<	u = sqrt( uSqr );
237	<	ux = ux / u;
238	<	uy = uy / u;
239	<	uz = uz / u;
240	<
241	<	dAtom->setSUx( ux );
242	<	dAtom->setSUy( uy );
243	<	dAtom->setSUz( uz );
244	<	}
245	<	else{
246	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
247	<	info[k].getConfiguration() );
248	<	}
249	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
250	<
219	>
220	>	for (j = 0; j < molInfo.nAtoms; j++){
221	>	currentAtom = comp_stamps[stampID]->getAtom(j);
222	>	if (currentAtom->haveOrientation()){
223	>	dAtom = new DirectionalAtom((j + atomOffset),
224	>	info[k].getConfiguration());
225	>	info[k].n_oriented++;
226	>	molInfo.myAtoms[j] = dAtom;
227	>
228	>	// Directional Atoms have standard unit vectors which are oriented
229	>	// in space using the three Euler angles.  We assume the standard
230	>	// unit vector was originally along the z axis below.
231	>
232	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
233	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
234	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
235	>
236	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
237	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
238	>	Axz = sin(theta) * sin(psi);
239	>
240	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
241	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
242	>	Ayz = sin(theta) * cos(psi);
243	>
244	>	Azx = sin(phi) * sin(theta);
245	>	Azy = -cos(phi) * sin(theta);
246	>	Azz = cos(theta);
247	>
248	>	sux = 0.0;
249	>	suy = 0.0;
250	>	suz = 1.0;
251	>
252	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
253	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
254	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
255	>
256	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257	>
258	>	u = sqrt(uSqr);
259	>	ux = ux / u;
260	>	uy = uy / u;
261	>	uz = uz / u;
262	>
263	>	dAtom->setSUx(ux);
264	>	dAtom->setSUy(uy);
265	>	dAtom->setSUz(uz);
266	>	}
267	>	else{
268	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
269	>	info[k].getConfiguration());
270	>	}
271	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
272	>
273		#ifdef IS_MPI
274	<
275	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
276	<
274	>
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
276	>
277		#endif // is_mpi
278		}
279	<
280	<	// make the bonds
281	<	for(j=0; j<molInfo.nBonds; j++){
282	<
283	<	currentBond = comp_stamps[stampID]->getBond( j );
284	<	theBonds[j].a = currentBond->getA() + atomOffset;
285	<	theBonds[j].b = currentBond->getB() + atomOffset;
286	<
287	<	exI = theBonds[j].a;
288	<	exJ = theBonds[j].b;
289	<
290	<	// exclude_I must always be the smaller of the pair
291	<	if( exI > exJ ){
292	<	tempEx = exI;
293	<	exI = exJ;
294	<	exJ = tempEx;
295	<	}
296	<	#ifdef IS_MPI
297	<	tempEx = exI;
298	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	<	tempEx = exJ;
300	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301	<
256	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
279	>
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285	>
286	>	exI = theBonds[j].a;
287	>	exJ = theBonds[j].b;
288	>
289	>	// exclude_I must always be the smaller of the pair
290	>	if (exI > exJ){
291	>	tempEx = exI;
292	>	exI = exJ;
293	>	exJ = tempEx;
294	>	}
295	>	#ifdef IS_MPI
296	>	tempEx = exI;
297	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
298	>	tempEx = exJ;
299	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
300	>
301	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
302		#else  // isn't MPI
303	<
304	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
303	>
304	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
305		#endif  //is_mpi
306		}
307		excludeOffset += molInfo.nBonds;
308	<
308	>
309		//make the bends
310	<	for(j=0; j<molInfo.nBends; j++){
311	<
312	<	currentBend = comp_stamps[stampID]->getBend( j );
313	<	theBends[j].a = currentBend->getA() + atomOffset;
314	<	theBends[j].b = currentBend->getB() + atomOffset;
315	<	theBends[j].c = currentBend->getC() + atomOffset;
316	<
317	<	if( currentBend->haveExtras() ){
318	<
319	<	extras = currentBend->getExtras();
320	<	current_extra = extras;
321	<
322	<	while( current_extra != NULL ){
323	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
324	<
325	<	switch( current_extra->getType() ){
326	<
327	<	case 0:
328	<	theBends[j].ghost =
329	<	current_extra->getInt() + atomOffset;
330	<	theBends[j].isGhost = 1;
331	<	break;
332	<
333	<	case 1:
334	<	theBends[j].ghost =
335	<	(int)current_extra->getDouble() + atomOffset;
336	<	theBends[j].isGhost = 1;
337	<	break;
338	<
339	<	default:
340	<	sprintf( painCave.errMsg,
341	<	"SimSetup Error: ghostVectorSource was neither a "
342	<	"double nor an int.\n"
343	<	"-->Bend[%d] in %s\n",
344	<	j, comp_stamps[stampID]->getID() );
345	<	painCave.isFatal = 1;
346	<	simError();
347	<	}
348	<	}
349	<
350	<	else{
351	<
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup Error: unhandled bend assignment:\n"
354	<	"    -->%s in Bend[%d] in %s\n",
355	<	current_extra->getlhs(),
356	<	j, comp_stamps[stampID]->getID() );
357	<	painCave.isFatal = 1;
358	<	simError();
359	<	}
360	<
361	<	current_extra = current_extra->getNext();
362	<	}
363	<	}
364	<
365	<	if( !theBends[j].isGhost ){
366	<
367	<	exI = theBends[j].a;
368	<	exJ = theBends[j].c;
369	<	}
370	<	else{
371	<
327	<	exI = theBends[j].a;
328	<	exJ = theBends[j].b;
329	<	}
330	<
331	<	// exclude_I must always be the smaller of the pair
332	<	if( exI > exJ ){
333	<	tempEx = exI;
334	<	exI = exJ;
335	<	exJ = tempEx;
336	<	}
310	>	for (j = 0; j < molInfo.nBends; j++){
311	>	currentBend = comp_stamps[stampID]->getBend(j);
312	>	theBends[j].a = currentBend->getA() + atomOffset;
313	>	theBends[j].b = currentBend->getB() + atomOffset;
314	>	theBends[j].c = currentBend->getC() + atomOffset;
315	>
316	>	if (currentBend->haveExtras()){
317	>	extras = currentBend->getExtras();
318	>	current_extra = extras;
319	>
320	>	while (current_extra != NULL){
321	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
322	>	switch (current_extra->getType()){
323	>	case 0:
324	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327	>
328	>	case 1:
329	>	theBends[j].ghost = (int) current_extra->getDouble() +
330	>	atomOffset;
331	>	theBends[j].isGhost = 1;
332	>	break;
333	>
334	>	default:
335	>	sprintf(painCave.errMsg,
336	>	"SimSetup Error: ghostVectorSource was neither a "
337	>	"double nor an int.\n"
338	>	"-->Bend[%d] in %s\n",
339	>	j, comp_stamps[stampID]->getID());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343	>	}
344	>	else{
345	>	sprintf(painCave.errMsg,
346	>	"SimSetup Error: unhandled bend assignment:\n"
347	>	"    -->%s in Bend[%d] in %s\n",
348	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
349	>	painCave.isFatal = 1;
350	>	simError();
351	>	}
352	>
353	>	current_extra = current_extra->getNext();
354	>	}
355	>	}
356	>
357	>	if (!theBends[j].isGhost){
358	>	exI = theBends[j].a;
359	>	exJ = theBends[j].c;
360	>	}
361	>	else{
362	>	exI = theBends[j].a;
363	>	exJ = theBends[j].b;
364	>	}
365	>
366	>	// exclude_I must always be the smaller of the pair
367	>	if (exI > exJ){
368	>	tempEx = exI;
369	>	exI = exJ;
370	>	exJ = tempEx;
371	>	}
372		#ifdef IS_MPI
373	<	tempEx = exI;
374	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	<	tempEx = exJ;
376	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
377	<
378	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
373	>	tempEx = exI;
374	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>	tempEx = exJ;
376	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
377	>
378	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
379		#else  // isn't MPI
380	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
380	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
381		#endif  //is_mpi
382		}
383		excludeOffset += molInfo.nBends;
384	<
385	<	for(j=0; j<molInfo.nTorsions; j++){
386	<
387	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
388	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
389	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
390	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
391	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
392	<
393	<	exI = theTorsions[j].a;
394	<	exJ = theTorsions[j].d;
395	<
396	<	// exclude_I must always be the smaller of the pair
397	<	if( exI > exJ ){
398	<	tempEx = exI;
399	<	exI = exJ;
400	<	exJ = tempEx;
366	<	}
384	>
385	>	for (j = 0; j < molInfo.nTorsions; j++){
386	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
387	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
388	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
389	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
390	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
391	>
392	>	exI = theTorsions[j].a;
393	>	exJ = theTorsions[j].d;
394	>
395	>	// exclude_I must always be the smaller of the pair
396	>	if (exI > exJ){
397	>	tempEx = exI;
398	>	exI = exJ;
399	>	exJ = tempEx;
400	>	}
401		#ifdef IS_MPI
402	<	tempEx = exI;
403	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
404	<	tempEx = exJ;
405	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
406	<
407	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
402	>	tempEx = exI;
403	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
404	>	tempEx = exJ;
405	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
406	>
407	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
408		#else  // isn't MPI
409	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
409	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
410		#endif  //is_mpi
411		}
412		excludeOffset += molInfo.nTorsions;
413	<
414	<
413	>
414	>
415		// send the arrays off to the forceField for init.
382	–
383	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
384	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
385	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
386	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
387	–
388	–
389	–	info[k].molecules[i].initialize( molInfo );
416
417	<
417	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
418	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
419	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
420	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
421	>	theTorsions);
422	>
423	>
424	>	info[k].molecules[i].initialize(molInfo);
425	>
426	>
427		atomOffset += molInfo.nAtoms;
428		delete[] theBonds;
429		delete[] theBends;
430		delete[] theTorsions;
431		}
432		}
433	<
433	>
434		#ifdef IS_MPI
435	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
435	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
436		MPIcheckPoint();
437		#endif // is_mpi
438	<
438	>
439		// clean up the forcefield
440
441		the_ff->calcRcut();
442		the_ff->cleanMe();
408	–
443		}
444
445	<	void SimSetup::initFromBass( void ){
412	<
445	>	void SimSetup::initFromBass(void){
446		int i, j, k;
447		int n_cells;
448		double cellx, celly, cellz;
#	Line 423 | Line 456 | void SimSetup::initFromBass( void ){
456		vel[1] = 0.0;
457		vel[2] = 0.0;
458
459	<	temp1 = (double)tot_nmol / 4.0;
460	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
461	<	temp3 = ceil( temp2 );
459	>	temp1 = (double) tot_nmol / 4.0;
460	>	temp2 = pow(temp1, (1.0 / 3.0));
461	>	temp3 = ceil(temp2);
462
463	<	have_extra =0;
464	<	if( temp2 < temp3 ){ // we have a non-complete lattice
465	<	have_extra =1;
463	>	have_extra = 0;
464	>	if (temp2 < temp3){
465	>	// we have a non-complete lattice
466	>	have_extra = 1;
467
468	<	n_cells = (int)temp3 - 1;
468	>	n_cells = (int) temp3 - 1;
469		cellx = info[0].boxL[0] / temp3;
470		celly = info[0].boxL[1] / temp3;
471		cellz = info[0].boxL[2] / temp3;
472	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
473	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
474	<	n_per_extra = (int)ceil( temp1 );
472	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
473	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
474	>	n_per_extra = (int) ceil(temp1);
475
476	<	if( n_per_extra > 4){
477	<	sprintf( painCave.errMsg,
478	<	"SimSetup error. There has been an error in constructing"
479	<	" the non-complete lattice.\n" );
476	>	if (n_per_extra > 4){
477	>	sprintf(painCave.errMsg,
478	>	"SimSetup error. There has been an error in constructing"
479	>	" the non-complete lattice.\n");
480		painCave.isFatal = 1;
481		simError();
482		}
483		}
484		else{
485	<	n_cells = (int)temp3;
485	>	n_cells = (int) temp3;
486		cellx = info[0].boxL[0] / temp3;
487		celly = info[0].boxL[1] / temp3;
488		cellz = info[0].boxL[2] / temp3;
#	Line 459 | Line 493 | void SimSetup::initFromBass( void ){
493		current_comp = 0;
494		current_atom_ndx = 0;
495
496	<	for( i=0; i < n_cells ; i++ ){
497	<	for( j=0; j < n_cells; j++ ){
498	<	for( k=0; k < n_cells; k++ ){
496	>	for (i = 0; i < n_cells ; i++){
497	>	for (j = 0; j < n_cells; j++){
498	>	for (k = 0; k < n_cells; k++){
499	>	makeElement(i * cellx, j * celly, k * cellz);
500
501	<	makeElement( i * cellx,
467	<	j * celly,
468	<	k * cellz );
501	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
502
503	<	makeElement( i * cellx + 0.5 * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz );
503	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
504
505	<	makeElement( i * cellx,
475	<	j * celly + 0.5 * celly,
476	<	k * cellz + 0.5 * cellz );
477	<
478	<	makeElement( i * cellx + 0.5 * cellx,
479	<	j * celly,
480	<	k * cellz + 0.5 * cellz );
505	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
506		}
507		}
508		}
509
510	<	if( have_extra ){
510	>	if (have_extra){
511		done = 0;
512
513		int start_ndx;
514	<	for( i=0; i < (n_cells+1) && !done; i++ ){
515	<	for( j=0; j < (n_cells+1) && !done; j++ ){
514	>	for (i = 0; i < (n_cells + 1) && !done; i++){
515	>	for (j = 0; j < (n_cells + 1) && !done; j++){
516	>	if (i < n_cells){
517	>	if (j < n_cells){
518	>	start_ndx = n_cells;
519	>	}
520	>	else
521	>	start_ndx = 0;
522	>	}
523	>	else
524	>	start_ndx = 0;
525
526	<	if( i < n_cells ){
526	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
527	>	makeElement(i * cellx, j * celly, k * cellz);
528	>	done = (current_mol >= tot_nmol);
529
530	<	if( j < n_cells ){
531	<	start_ndx = n_cells;
532	<	}
533	<	else start_ndx = 0;
534	<	}
499	<	else start_ndx = 0;
530	>	if (!done && n_per_extra > 1){
531	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
532	>	k * cellz);
533	>	done = (current_mol >= tot_nmol);
534	>	}
535
536	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
536	>	if (!done && n_per_extra > 2){
537	>	makeElement(i * cellx, j * celly + 0.5 * celly,
538	>	k * cellz + 0.5 * cellz);
539	>	done = (current_mol >= tot_nmol);
540	>	}
541
542	<	makeElement( i * cellx,
543	<	j * celly,
544	<	k * cellz );
545	<	done = ( current_mol >= tot_nmol );
546	<
547	<	if( !done && n_per_extra > 1 ){
509	<	makeElement( i * cellx + 0.5 * cellx,
510	<	j * celly + 0.5 * celly,
511	<	k * cellz );
512	<	done = ( current_mol >= tot_nmol );
513	<	}
514	<
515	<	if( !done && n_per_extra > 2){
516	<	makeElement( i * cellx,
517	<	j * celly + 0.5 * celly,
518	<	k * cellz + 0.5 * cellz );
519	<	done = ( current_mol >= tot_nmol );
520	<	}
521	<
522	<	if( !done && n_per_extra > 3){
523	<	makeElement( i * cellx + 0.5 * cellx,
524	<	j * celly,
525	<	k * cellz + 0.5 * cellz );
526	<	done = ( current_mol >= tot_nmol );
527	<	}
528	<	}
542	>	if (!done && n_per_extra > 3){
543	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
544	>	k * cellz + 0.5 * cellz);
545	>	done = (current_mol >= tot_nmol);
546	>	}
547	>	}
548		}
549		}
550		}
551
552	<	for( i=0; i<info[0].n_atoms; i++ ){
553	<	info[0].atoms[i]->setVel( vel );
552	>	for (i = 0; i < info[0].n_atoms; i++){
553	>	info[0].atoms[i]->setVel(vel);
554		}
555		}
556
557	<	void SimSetup::makeElement( double x, double y, double z ){
539	<
557	>	void SimSetup::makeElement(double x, double y, double z){
558		int k;
559		AtomStamp* current_atom;
560		DirectionalAtom* dAtom;
561		double rotMat[3][3];
562		double pos[3];
563
564	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
565	<
566	<	current_atom = comp_stamps[current_comp]->getAtom( k );
567	<	if( !current_atom->havePosition() ){
568	<	sprintf( painCave.errMsg,
569	<	"SimSetup:initFromBass error.\n"
570	<	"\tComponent %s, atom %s does not have a position specified.\n"
571	<	"\tThe initialization routine is unable to give a start"
572	<	" position.\n",
555	<	comp_stamps[current_comp]->getID(),
556	<	current_atom->getType() );
564	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
565	>	current_atom = comp_stamps[current_comp]->getAtom(k);
566	>	if (!current_atom->havePosition()){
567	>	sprintf(painCave.errMsg,
568	>	"SimSetup:initFromBass error.\n"
569	>	"\tComponent %s, atom %s does not have a position specified.\n"
570	>	"\tThe initialization routine is unable to give a start"
571	>	" position.\n",
572	>	comp_stamps[current_comp]->getID(), current_atom->getType());
573		painCave.isFatal = 1;
574		simError();
575		}
576	<
576	>
577		pos[0] = x + current_atom->getPosX();
578		pos[1] = y + current_atom->getPosY();
579		pos[2] = z + current_atom->getPosZ();
564	–
565	–	info[0].atoms[current_atom_ndx]->setPos( pos );
580
581	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
581	>	info[0].atoms[current_atom_ndx]->setPos(pos);
582
583	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
583	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
584	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
585
586		rotMat[0][0] = 1.0;
587		rotMat[0][1] = 0.0;
#	Line 580 | Line 595 | void SimSetup::makeElement( double x, double y, double
595		rotMat[2][1] = 0.0;
596		rotMat[2][2] = 1.0;
597
598	<	dAtom->setA( rotMat );
598	>	dAtom->setA(rotMat);
599		}
600
601		current_atom_ndx++;
#	Line 589 | Line 604 | void SimSetup::makeElement( double x, double y, double
604		current_mol++;
605		current_comp_mol++;
606
607	<	if( current_comp_mol >= components_nmol[current_comp] ){
593	<
607	>	if (current_comp_mol >= components_nmol[current_comp]){
608		current_comp_mol = 0;
609		current_comp++;
610		}
611		}
612
613
614	<	void SimSetup::gatherInfo( void ){
615	<	int i,j,k;
614	>	void SimSetup::gatherInfo(void){
615	>	int i;
616
617		ensembleCase = -1;
618		ffCase = -1;
619
620		// set the easy ones first
621
622	<	for( i=0; i<nInfo; i++){
622	>	for (i = 0; i < nInfo; i++){
623		info[i].target_temp = globals->getTargetTemp();
624		info[i].dt = globals->getDt();
625		info[i].run_time = globals->getRunTime();
#	Line 615 | Line 629 | void SimSetup::gatherInfo( void ){
629
630		// get the forceField
631
632	<	strcpy( force_field, globals->getForceField() );
632	>	strcpy(force_field, globals->getForceField());
633
634	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
635	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
636	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
634	>	if (!strcasecmp(force_field, "DUFF")){
635	>	ffCase = FF_DUFF;
636	>	}
637	>	else if (!strcasecmp(force_field, "LJ")){
638	>	ffCase = FF_LJ;
639	>	}
640	>	else if (!strcasecmp(force_field, "EAM")){
641	>	ffCase = FF_EAM;
642	>	}
643	>	else if (!strcasecmp(force_field, "WATER")){
644	>	ffCase = FF_H2O;
645	>	}
646		else{
647	<	sprintf( painCave.errMsg,
648	<	"SimSetup Error. Unrecognized force field -> %s\n",
649	<	force_field );
650	<	painCave.isFatal = 1;
628	<	simError();
647	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
648	>	force_field);
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
652
653	<	// get the ensemble
653	>	// get the ensemble
654
655	<	strcpy( ensemble, globals->getEnsemble() );
655	>	strcpy(ensemble, globals->getEnsemble());
656
657	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
658	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
659	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
657	>	if (!strcasecmp(ensemble, "NVE")){
658	>	ensembleCase = NVE_ENS;
659	>	}
660	>	else if (!strcasecmp(ensemble, "NVT")){
661	>	ensembleCase = NVT_ENS;
662	>	}
663	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
664		ensembleCase = NPTi_ENS;
665	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
666	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
667	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
668	<
669	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
670	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
671	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	<	ensembleCase = NPTiZCONS_ENS;
647	<	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	<	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	<
665	>	}
666	>	else if (!strcasecmp(ensemble, "NPTf")){
667	>	ensembleCase = NPTf_ENS;
668	>	}
669	>	else if (!strcasecmp(ensemble, "NPTxyz")){
670	>	ensembleCase = NPTxyz_ENS;
671	>	}
672		else{
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
675	<	"reverting to NVE for this simulation.\n",
676	<	ensemble );
677	<	painCave.isFatal = 0;
678	<	simError();
679	<	strcpy( ensemble, "NVE" );
680	<	ensembleCase = NVE_ENS;
673	>	sprintf(painCave.errMsg,
674	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
675	>	"\treverting to NVE for this simulation.\n",
676	>	ensemble);
677	>	painCave.isFatal = 0;
678	>	simError();
679	>	strcpy(ensemble, "NVE");
680	>	ensembleCase = NVE_ENS;
681		}
661	–
662	–	for(i=0; i<nInfo; i++){
663	–
664	–	strcpy( info[i].ensemble, ensemble );
682
683	+	for (i = 0; i < nInfo; i++){
684	+	strcpy(info[i].ensemble, ensemble);
685	+
686		// get the mixing rule
687
688	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
688	>	strcpy(info[i].mixingRule, globals->getMixingRule());
689		info[i].usePBC = globals->getPBC();
690		}
691	<
691	>
692		// get the components and calculate the tot_nMol and indvidual n_mol
693	<
693	>
694		the_components = globals->getComponents();
695		components_nmol = new int[n_components];
696
697
698	<	if( !globals->haveNMol() ){
698	>	if (!globals->haveNMol()){
699		// we don't have the total number of molecules, so we assume it is
700		// given in each component
701
702		tot_nmol = 0;
703	<	for( i=0; i<n_components; i++ ){
704	<
705	<	if( !the_components[i]->haveNMol() ){
706	<	// we have a problem
707	<	sprintf( painCave.errMsg,
708	<	"SimSetup Error. No global NMol or component NMol"
709	<	" given. Cannot calculate the number of atoms.\n" );
710	<	painCave.isFatal = 1;
691	<	simError();
703	>	for (i = 0; i < n_components; i++){
704	>	if (!the_components[i]->haveNMol()){
705	>	// we have a problem
706	>	sprintf(painCave.errMsg,
707	>	"SimSetup Error. No global NMol or component NMol given.\n"
708	>	"\tCannot calculate the number of atoms.\n");
709	>	painCave.isFatal = 1;
710	>	simError();
711		}
712
713		tot_nmol += the_components[i]->getNMol();
#	Line 696 | Line 715 | void SimSetup::gatherInfo( void ){
715		}
716		}
717		else{
718	<	sprintf( painCave.errMsg,
719	<	"SimSetup error.\n"
720	<	"\tSorry, the ability to specify total"
721	<	" nMols and then give molfractions in the components\n"
722	<	"\tis not currently supported."
723	<	" Please give nMol in the components.\n" );
718	>	sprintf(painCave.errMsg,
719	>	"SimSetup error.\n"
720	>	"\tSorry, the ability to specify total"
721	>	" nMols and then give molfractions in the components\n"
722	>	"\tis not currently supported."
723	>	" Please give nMol in the components.\n");
724		painCave.isFatal = 1;
725		simError();
726		}
727
728	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
729	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
730	+	sprintf(painCave.errMsg,
731	+	"Sample time is not divisible by dt.\n"
732	+	"\tThis will result in samples that are not uniformly\n"
733	+	"\tdistributed in time.  If this is a problem, change\n"
734	+	"\tyour sampleTime variable.\n");
735	+	painCave.isFatal = 0;
736	+	simError();
737	+	}
738	+
739	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
740	+	sprintf(painCave.errMsg,
741	+	"Status time is not divisible by dt.\n"
742	+	"\tThis will result in status reports that are not uniformly\n"
743	+	"\tdistributed in time.  If this is a problem, change \n"
744	+	"\tyour statusTime variable.\n");
745	+	painCave.isFatal = 0;
746	+	simError();
747	+	}
748	+
749	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
750	+	sprintf(painCave.errMsg,
751	+	"Thermal time is not divisible by dt.\n"
752	+	"\tThis will result in thermalizations that are not uniformly\n"
753	+	"\tdistributed in time.  If this is a problem, change \n"
754	+	"\tyour thermalTime variable.\n");
755	+	painCave.isFatal = 0;
756	+	simError();
757	+	}
758	+
759	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
760	+	sprintf(painCave.errMsg,
761	+	"Reset time is not divisible by dt.\n"
762	+	"\tThis will result in integrator resets that are not uniformly\n"
763	+	"\tdistributed in time.  If this is a problem, change\n"
764	+	"\tyour resetTime variable.\n");
765	+	painCave.isFatal = 0;
766	+	simError();
767	+	}
768	+
769		// set the status, sample, and thermal kick times
710	–
711	–	for(i=0; i<nInfo; i++){
770
771	<	if( globals->haveSampleTime() ){
771	>	for (i = 0; i < nInfo; i++){
772	>	if (globals->haveSampleTime()){
773		info[i].sampleTime = globals->getSampleTime();
774		info[i].statusTime = info[i].sampleTime;
775		info[i].thermalTime = info[i].sampleTime;
#	Line 720 | Line 779 | void SimSetup::gatherInfo( void ){
779		info[i].statusTime = info[i].sampleTime;
780		info[i].thermalTime = info[i].sampleTime;
781		}
782	<
783	<	if( globals->haveStatusTime() ){
782	>
783	>	if (globals->haveStatusTime()){
784		info[i].statusTime = globals->getStatusTime();
785		}
786	<
787	<	if( globals->haveThermalTime() ){
786	>
787	>	if (globals->haveThermalTime()){
788		info[i].thermalTime = globals->getThermalTime();
789		}
790
791	+	info[i].resetIntegrator = 0;
792	+	if( globals->haveResetTime() ){
793	+	info[i].resetTime = globals->getResetTime();
794	+	info[i].resetIntegrator = 1;
795	+	}
796	+
797		// check for the temperature set flag
798	+
799	+	if (globals->haveTempSet())
800	+	info[i].setTemp = globals->getTempSet();
801
802	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
802	>	// check for the extended State init
803	>
804	>	info[i].useInitXSstate = globals->getUseInitXSstate();
805	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
806
736	–	// get some of the tricky things that may still be in the globals
737	–
738	–	double boxVector[3];
739	–	if( globals->haveBox() ){
740	–	boxVector[0] = globals->getBox();
741	–	boxVector[1] = globals->getBox();
742	–	boxVector[2] = globals->getBox();
743	–
744	–	info[i].setBox( boxVector );
745	–	}
746	–	else if( globals->haveDensity() ){
747	–
748	–	double vol;
749	–	vol = (double)tot_nmol / globals->getDensity();
750	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	–	boxVector[1] = boxVector[0];
752	–	boxVector[2] = boxVector[0];
753	–
754	–	info[i].setBox( boxVector );
807		}
808	<	else{
809	<	if( !globals->haveBoxX() ){
810	<	sprintf( painCave.errMsg,
811	<	"SimSetup error, no periodic BoxX size given.\n" );
812	<	painCave.isFatal = 1;
813	<	simError();
808	>
809	>	//setup seed for random number generator
810	>	int seedValue;
811	>
812	>	if (globals->haveSeed()){
813	>	seedValue = globals->getSeed();
814	>
815	>	if(seedValue / 1E9 == 0){
816	>	sprintf(painCave.errMsg,
817	>	"Seed for sprng library should contain at least 9 digits\n"
818	>	"OOPSE will generate a seed for user\n");
819	>	painCave.isFatal = 0;
820	>	simError();
821	>
822	>	//using seed generated by system instead of invalid seed set by user
823	>	#ifndef IS_MPI
824	>	seedValue = make_sprng_seed();
825	>	#else
826	>	if (worldRank == 0){
827	>	seedValue = make_sprng_seed();
828		}
829	<	boxVector[0] = globals->getBoxX();
830	<
765	<	if( !globals->haveBoxY() ){
766	<	sprintf( painCave.errMsg,
767	<	"SimSetup error, no periodic BoxY size given.\n" );
768	<	painCave.isFatal = 1;
769	<	simError();
770	<	}
771	<	boxVector[1] = globals->getBoxY();
772	<
773	<	if( !globals->haveBoxZ() ){
774	<	sprintf( painCave.errMsg,
775	<	"SimSetup error, no periodic BoxZ size given.\n" );
776	<	painCave.isFatal = 1;
777	<	simError();
778	<	}
779	<	boxVector[2] = globals->getBoxZ();
780	<
781	<	info[i].setBox( boxVector );
829	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
830	>	#endif
831		}
832	+	}//end of if branch of globals->haveSeed()
833	+	else{
834	+
835	+	#ifndef IS_MPI
836	+	seedValue = make_sprng_seed();
837	+	#else
838	+	if (worldRank == 0){
839	+	seedValue = make_sprng_seed();
840	+	}
841	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
842	+	#endif
843	+	}//end of globals->haveSeed()
844
845	+	for (int i = 0; i < nInfo; i++){
846	+	info[i].setSeed(seedValue);
847		}
848	<
848	>
849		#ifdef IS_MPI
850	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
850	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
851		MPIcheckPoint();
852		#endif // is_mpi
790	–
853		}
854
855
856	<	void SimSetup::finalInfoCheck( void ){
856	>	void SimSetup::finalInfoCheck(void){
857		int index;
858		int usesDipoles;
859		int i;
860
861	<	for(i=0; i<nInfo; i++){
861	>	for (i = 0; i < nInfo; i++){
862		// check electrostatic parameters
863	<
863	>
864		index = 0;
865		usesDipoles = 0;
866	<	while( (index < info[i].n_atoms) && !usesDipoles ){
866	>	while ((index < info[i].n_atoms) && !usesDipoles){
867		usesDipoles = (info[i].atoms[index])->hasDipole();
868		index++;
869		}
870	<
870	>
871		#ifdef IS_MPI
872		int myUse = usesDipoles;
873	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
873	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874		#endif //is_mpi
875	<
875	>
876		double theEcr, theEst;
877	<
878	<	if (globals->getUseRF() ) {
877	>
878	>	if (globals->getUseRF()){
879		info[i].useReactionField = 1;
880	<
881	<	if( !globals->haveECR() ){
882	<	sprintf( painCave.errMsg,
883	<	"SimSetup Warning: using default value of 1/2 the smallest "
884	<	"box length for the electrostaticCutoffRadius.\n"
885	<	"I hope you have a very fast processor!\n");
886	<	painCave.isFatal = 0;
887	<	simError();
888	<	double smallest;
827	<	smallest = info[i].boxL[0];
828	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830	<	theEcr = 0.5 * smallest;
831	<	} else {
832	<	theEcr = globals->getECR();
880	>
881	>	if (!globals->haveECR()){
882	>	sprintf(painCave.errMsg,
883	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
884	>	"\tOOPSE will use a default value of 15.0 angstroms"
885	>	"\tfor the electrostaticCutoffRadius.\n");
886	>	painCave.isFatal = 0;
887	>	simError();
888	>	theEcr = 15.0;
889		}
890	<
891	<	if( !globals->haveEST() ){
836	<	sprintf( painCave.errMsg,
837	<	"SimSetup Warning: using default value of 0.05 * the "
838	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	<	);
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	theEst = 0.05 * theEcr;
843	<	} else {
844	<	theEst= globals->getEST();
890	>	else{
891	>	theEcr = globals->getECR();
892		}
893	<
894	<	info[i].setEcr( theEcr, theEst );
895	<
896	<	if(!globals->haveDielectric() ){
897	<	sprintf( painCave.errMsg,
898	<	"SimSetup Error: You are trying to use Reaction Field without"
899	<	"setting a dielectric constant!\n"
900	<	);
901	<	painCave.isFatal = 1;
902	<	simError();
893	>
894	>	if (!globals->haveEST()){
895	>	sprintf(painCave.errMsg,
896	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
897	>	"\tOOPSE will use a default value of\n"
898	>	"\t0.05 * electrostaticCutoffRadius\n"
899	>	"\tfor the electrostaticSkinThickness\n");
900	>	painCave.isFatal = 0;
901	>	simError();
902	>	theEst = 0.05 * theEcr;
903		}
904	<	info[i].dielectric = globals->getDielectric();
905	<	}
906	<	else {
907	<	if (usesDipoles) {
908	<
909	<	if( !globals->haveECR() ){
910	<	sprintf( painCave.errMsg,
911	<	"SimSetup Warning: using default value of 1/2 the smallest "
912	<	"box length for the electrostaticCutoffRadius.\n"
913	<	"I hope you have a very fast processor!\n");
904	>	else{
905	>	theEst = globals->getEST();
906	>	}
907	>
908	>	info[i].setDefaultEcr(theEcr, theEst);
909	>
910	>	if (!globals->haveDielectric()){
911	>	sprintf(painCave.errMsg,
912	>	"SimSetup Error: No Dielectric constant was set.\n"
913	>	"\tYou are trying to use Reaction Field without"
914	>	"\tsetting a dielectric constant!\n");
915	>	painCave.isFatal = 1;
916	>	simError();
917	>	}
918	>	info[i].dielectric = globals->getDielectric();
919	>	}
920	>	else{
921	>	if (usesDipoles){
922	>	if (!globals->haveECR()){
923	>	sprintf(painCave.errMsg,
924	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
925	>	"\tOOPSE will use a default value of 15.0 angstroms"
926	>	"\tfor the electrostaticCutoffRadius.\n");
927		painCave.isFatal = 0;
928		simError();
929	<	double smallest;
930	<	smallest = info[i].boxL[0];
931	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
932	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
933	<	theEcr = 0.5 * smallest;
874	<	} else {
875	<	theEcr = globals->getECR();
876	<	}
929	>	theEcr = 15.0;
930	>	}
931	>	else{
932	>	theEcr = globals->getECR();
933	>	}
934
935	<	if( !globals->haveEST() ){
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Warning: using default value of 0.05 * the "
938	<	"electrostaticCutoffRadius for the "
939	<	"electrostaticSkinThickness\n"
940	<	);
941	<	painCave.isFatal = 0;
942	<	simError();
943	<	theEst = 0.05 * theEcr;
944	<	} else {
945	<	theEst= globals->getEST();
946	<	}
935	>	if (!globals->haveEST()){
936	>	sprintf(painCave.errMsg,
937	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
938	>	"\tOOPSE will use a default value of\n"
939	>	"\t0.05 * electrostaticCutoffRadius\n"
940	>	"\tfor the electrostaticSkinThickness\n");
941	>	painCave.isFatal = 0;
942	>	simError();
943	>	theEst = 0.05 * theEcr;
944	>	}
945	>	else{
946	>	theEst = globals->getEST();
947	>	}
948
949	<	info[i].setEcr( theEcr, theEst );
949	>	info[i].setDefaultEcr(theEcr, theEst);
950		}
951	<	}
951	>	}
952		}
895	–
953		#ifdef IS_MPI
954	<	strcpy( checkPointMsg, "post processing checks out" );
954	>	strcpy(checkPointMsg, "post processing checks out");
955		MPIcheckPoint();
956		#endif // is_mpi
900	–
957		}
902	–
903	–	void SimSetup::initSystemCoords( void ){
904	–	int i;
958
959	<	std::cerr << "Setting atom Coords\n";
959	>	void SimSetup::initSystemCoords(void){
960	>	int i;
961
962	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
963	<
964	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
965	<
966	<	if( globals->haveInitialConfig() ){
967	<
962	>	char* inName;
963	>
964	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
965	>
966	>	for (i = 0; i < info[0].n_atoms; i++)
967	>	info[0].atoms[i]->setCoords();
968	>
969	>	if (globals->haveInitialConfig()){
970		InitializeFromFile* fileInit;
971		#ifdef IS_MPI // is_mpi
972	<	if( worldRank == 0 ){
972	>	if (worldRank == 0){
973		#endif //is_mpi
974	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
974	>	inName = globals->getInitialConfig();
975	>	fileInit = new InitializeFromFile(inName);
976		#ifdef IS_MPI
977	<	}else fileInit = new InitializeFromFile( NULL );
977	>	}
978	>	else
979	>	fileInit = new InitializeFromFile(NULL);
980		#endif
981	<	fileInit->readInit( info ); // default velocities on
982	<
981	>	fileInit->readInit(info); // default velocities on
982	>
983		delete fileInit;
984		}
985		else{
986
928	–	#ifdef IS_MPI
929	–
987		// no init from bass
988
989	<	sprintf( painCave.errMsg,
990	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
991	<	painCave.isFatal;
989	>	sprintf(painCave.errMsg,
990	>	"Cannot intialize a simulation without an initial configuration file.\n");
991	>	painCave.isFatal = 1;;
992		simError();
993
937	–	#else
938	–
939	–	initFromBass();
940	–
941	–
942	–	#endif
994		}
995	<
995	>
996		#ifdef IS_MPI
997	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
997	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
998		MPIcheckPoint();
999		#endif // is_mpi
949	–
1000		}
1001
1002
1003	<	void SimSetup::makeOutNames( void ){
954	<
1003	>	void SimSetup::makeOutNames(void){
1004		int k;
1005
957	–
958	–	for(k=0; k<nInfo; k++){
1006
1007	+	for (k = 0; k < nInfo; k++){
1008		#ifdef IS_MPI
1009	<	if( worldRank == 0 ){
1009	>	if (worldRank == 0){
1010		#endif // is_mpi
1011	<
1012	<	if( globals->haveFinalConfig() ){
1013	<	strcpy( info[k].finalName, globals->getFinalConfig() );
1011	>
1012	>	if (globals->haveFinalConfig()){
1013	>	strcpy(info[k].finalName, globals->getFinalConfig());
1014		}
1015		else{
1016	<	strcpy( info[k].finalName, inFileName );
1017	<	char* endTest;
1018	<	int nameLength = strlen( info[k].finalName );
1019	<	endTest = &(info[k].finalName[nameLength - 5]);
1020	<	if( !strcmp( endTest, ".bass" ) ){
1021	<	strcpy( endTest, ".eor" );
1022	<	}
1023	<	else if( !strcmp( endTest, ".BASS" ) ){
1024	<	strcpy( endTest, ".eor" );
1025	<	}
1026	<	else{
1027	<	endTest = &(info[k].finalName[nameLength - 4]);
1028	<	if( !strcmp( endTest, ".bss" ) ){
1029	<	strcpy( endTest, ".eor" );
1030	<	}
1031	<	else if( !strcmp( endTest, ".mdl" ) ){
1032	<	strcpy( endTest, ".eor" );
1033	<	}
1034	<	else{
1035	<	strcat( info[k].finalName, ".eor" );
1036	<	}
1037	<	}
1038	<	}
1039	<
1040	<	// make the sample and status out names
1041	<
1042	<	strcpy( info[k].sampleName, inFileName );
1043	<	char* endTest;
1044	<	int nameLength = strlen( info[k].sampleName );
1016	>	strcpy(info[k].finalName, inFileName);
1017	>	char* endTest;
1018	>	int nameLength = strlen(info[k].finalName);
1019	>	endTest = &(info[k].finalName[nameLength - 5]);
1020	>	if (!strcmp(endTest, ".bass")){
1021	>	strcpy(endTest, ".eor");
1022	>	}
1023	>	else if (!strcmp(endTest, ".BASS")){
1024	>	strcpy(endTest, ".eor");
1025	>	}
1026	>	else{
1027	>	endTest = &(info[k].finalName[nameLength - 4]);
1028	>	if (!strcmp(endTest, ".bss")){
1029	>	strcpy(endTest, ".eor");
1030	>	}
1031	>	else if (!strcmp(endTest, ".mdl")){
1032	>	strcpy(endTest, ".eor");
1033	>	}
1034	>	else{
1035	>	strcat(info[k].finalName, ".eor");
1036	>	}
1037	>	}
1038	>	}
1039	>
1040	>	// make the sample and status out names
1041	>
1042	>	strcpy(info[k].sampleName, inFileName);
1043	>	char* endTest;
1044	>	int nameLength = strlen(info[k].sampleName);
1045		endTest = &(info[k].sampleName[nameLength - 5]);
1046	<	if( !strcmp( endTest, ".bass" ) ){
1047	<	strcpy( endTest, ".dump" );
1046	>	if (!strcmp(endTest, ".bass")){
1047	>	strcpy(endTest, ".dump");
1048		}
1049	<	else if( !strcmp( endTest, ".BASS" ) ){
1050	<	strcpy( endTest, ".dump" );
1049	>	else if (!strcmp(endTest, ".BASS")){
1050	>	strcpy(endTest, ".dump");
1051		}
1052		else{
1053	<	endTest = &(info[k].sampleName[nameLength - 4]);
1054	<	if( !strcmp( endTest, ".bss" ) ){
1055	<	strcpy( endTest, ".dump" );
1056	<	}
1057	<	else if( !strcmp( endTest, ".mdl" ) ){
1058	<	strcpy( endTest, ".dump" );
1059	<	}
1060	<	else{
1061	<	strcat( info[k].sampleName, ".dump" );
1062	<	}
1053	>	endTest = &(info[k].sampleName[nameLength - 4]);
1054	>	if (!strcmp(endTest, ".bss")){
1055	>	strcpy(endTest, ".dump");
1056	>	}
1057	>	else if (!strcmp(endTest, ".mdl")){
1058	>	strcpy(endTest, ".dump");
1059	>	}
1060	>	else{
1061	>	strcat(info[k].sampleName, ".dump");
1062	>	}
1063		}
1064	<
1065	<	strcpy( info[k].statusName, inFileName );
1066	<	nameLength = strlen( info[k].statusName );
1064	>
1065	>	strcpy(info[k].statusName, inFileName);
1066	>	nameLength = strlen(info[k].statusName);
1067		endTest = &(info[k].statusName[nameLength - 5]);
1068	<	if( !strcmp( endTest, ".bass" ) ){
1069	<	strcpy( endTest, ".stat" );
1068	>	if (!strcmp(endTest, ".bass")){
1069	>	strcpy(endTest, ".stat");
1070		}
1071	<	else if( !strcmp( endTest, ".BASS" ) ){
1072	<	strcpy( endTest, ".stat" );
1071	>	else if (!strcmp(endTest, ".BASS")){
1072	>	strcpy(endTest, ".stat");
1073		}
1074		else{
1075	<	endTest = &(info[k].statusName[nameLength - 4]);
1076	<	if( !strcmp( endTest, ".bss" ) ){
1077	<	strcpy( endTest, ".stat" );
1078	<	}
1079	<	else if( !strcmp( endTest, ".mdl" ) ){
1080	<	strcpy( endTest, ".stat" );
1081	<	}
1082	<	else{
1083	<	strcat( info[k].statusName, ".stat" );
1084	<	}
1075	>	endTest = &(info[k].statusName[nameLength - 4]);
1076	>	if (!strcmp(endTest, ".bss")){
1077	>	strcpy(endTest, ".stat");
1078	>	}
1079	>	else if (!strcmp(endTest, ".mdl")){
1080	>	strcpy(endTest, ".stat");
1081	>	}
1082	>	else{
1083	>	strcat(info[k].statusName, ".stat");
1084	>	}
1085		}
1086	<
1086	>
1087		#ifdef IS_MPI
1088	+
1089		}
1090		#endif // is_mpi
1091		}
1092		}
1093
1094
1095	<	void SimSetup::sysObjectsCreation( void ){
1096	<
1097	<	int i,k;
1049	<
1095	>	void SimSetup::sysObjectsCreation(void){
1096	>	int i, k;
1097	>
1098		// create the forceField
1099	<
1099	>
1100		createFF();
1101
1102		// extract componentList
#	Line 1061 | Line 1109 | void SimSetup::sysObjectsCreation( void ){
1109
1110		#ifdef IS_MPI
1111		// divide the molecules among the processors
1112	<
1112	>
1113		mpiMolDivide();
1114		#endif //is_mpi
1115	<
1115	>
1116		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1117	<
1117	>
1118		makeSysArrays();
1119
1120		// make and initialize the molecules (all but atomic coordinates)
1121	<
1121	>
1122		makeMolecules();
1123	<
1124	<	for(k=0; k<nInfo; k++){
1123	>
1124	>	for (k = 0; k < nInfo; k++){
1125		info[k].identArray = new int[info[k].n_atoms];
1126	<	for(i=0; i<info[k].n_atoms; i++){
1126	>	for (i = 0; i < info[k].n_atoms; i++){
1127		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1128		}
1129		}
1130		}
1131
1132
1133	<	void SimSetup::createFF( void ){
1133	>	void SimSetup::createFF(void){
1134	>	switch (ffCase){
1135	>	case FF_DUFF:
1136	>	the_ff = new DUFF();
1137	>	break;
1138
1139	<	switch( ffCase ){
1139	>	case FF_LJ:
1140	>	the_ff = new LJFF();
1141	>	break;
1142
1143	<	case FF_DUFF:
1144	<	the_ff = new DUFF();
1145	<	break;
1143	>	case FF_EAM:
1144	>	the_ff = new EAM_FF();
1145	>	break;
1146
1147	<	case FF_LJ:
1148	<	the_ff = new LJFF();
1149	<	break;
1147	>	case FF_H2O:
1148	>	the_ff = new WATER();
1149	>	break;
1150
1151	<	case FF_EAM:
1152	<	the_ff = new EAM_FF();
1153	<	break;
1154	<
1155	<	default:
1102	<	sprintf( painCave.errMsg,
1103	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1104	<	painCave.isFatal = 1;
1105	<	simError();
1151	>	default:
1152	>	sprintf(painCave.errMsg,
1153	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1154	>	painCave.isFatal = 1;
1155	>	simError();
1156		}
1157
1158		#ifdef IS_MPI
1159	<	strcpy( checkPointMsg, "ForceField creation successful" );
1159	>	strcpy(checkPointMsg, "ForceField creation successful");
1160		MPIcheckPoint();
1161		#endif // is_mpi
1112	–
1162		}
1163
1164
1165	<	void SimSetup::compList( void ){
1117	<
1165	>	void SimSetup::compList(void){
1166		int i;
1167		char* id;
1168		LinkedMolStamp* headStamp = new LinkedMolStamp();
1169		LinkedMolStamp* currentStamp = NULL;
1170	<	comp_stamps = new MoleculeStamp*[n_components];
1171	<
1170	>	comp_stamps = new MoleculeStamp * [n_components];
1171	>
1172		// make an array of molecule stamps that match the components used.
1173		// also extract the used stamps out into a separate linked list
1174	<
1175	<	for(i=0; i<nInfo; i++){
1174	>
1175	>	for (i = 0; i < nInfo; i++){
1176		info[i].nComponents = n_components;
1177		info[i].componentsNmol = components_nmol;
1178		info[i].compStamps = comp_stamps;
1179		info[i].headStamp = headStamp;
1180		}
1133	–
1181
1135	–	for( i=0; i<n_components; i++ ){
1182
1183	+	for (i = 0; i < n_components; i++){
1184		id = the_components[i]->getType();
1185		comp_stamps[i] = NULL;
1186	<
1186	>
1187		// check to make sure the component isn't already in the list
1188
1189	<	comp_stamps[i] = headStamp->match( id );
1190	<	if( comp_stamps[i] == NULL ){
1144	<
1189	>	comp_stamps[i] = headStamp->match(id);
1190	>	if (comp_stamps[i] == NULL){
1191		// extract the component from the list;
1192	<
1193	<	currentStamp = stamps->extractMolStamp( id );
1194	<	if( currentStamp == NULL ){
1195	<	sprintf( painCave.errMsg,
1196	<	"SimSetup error: Component \"%s\" was not found in the "
1197	<	"list of declared molecules\n",
1198	<	id );
1199	<	painCave.isFatal = 1;
1200	<	simError();
1192	>
1193	>	currentStamp = stamps->extractMolStamp(id);
1194	>	if (currentStamp == NULL){
1195	>	sprintf(painCave.errMsg,
1196	>	"SimSetup error: Component \"%s\" was not found in the "
1197	>	"list of declared molecules\n",
1198	>	id);
1199	>	painCave.isFatal = 1;
1200	>	simError();
1201		}
1202	<
1203	<	headStamp->add( currentStamp );
1204	<	comp_stamps[i] = headStamp->match( id );
1202	>
1203	>	headStamp->add(currentStamp);
1204	>	comp_stamps[i] = headStamp->match(id);
1205		}
1206		}
1207
1208		#ifdef IS_MPI
1209	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1209	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1210		MPIcheckPoint();
1211		#endif // is_mpi
1212	+	}
1213
1214	+	void SimSetup::calcSysValues(void){
1215	+	int i;
1216
1217	<	}
1217	>	int* molMembershipArray;
1218
1170	–	void SimSetup::calcSysValues( void ){
1171	–	int i, j, k;
1172	–
1173	–	int *molMembershipArray;
1174	–
1219		tot_atoms = 0;
1220		tot_bonds = 0;
1221		tot_bends = 0;
1222		tot_torsions = 0;
1223	<	for( i=0; i<n_components; i++ ){
1224	<
1225	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1226	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1183	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1223	>	for (i = 0; i < n_components; i++){
1224	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1225	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1226	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1227		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1228		}
1229	<
1229	>
1230		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1231		molMembershipArray = new int[tot_atoms];
1232	<
1233	<	for(i=0; i<nInfo; i++){
1232	>
1233	>	for (i = 0; i < nInfo; i++){
1234		info[i].n_atoms = tot_atoms;
1235		info[i].n_bonds = tot_bonds;
1236		info[i].n_bends = tot_bends;
1237		info[i].n_torsions = tot_torsions;
1238		info[i].n_SRI = tot_SRI;
1239		info[i].n_mol = tot_nmol;
1240	<
1240	>
1241		info[i].molMembershipArray = molMembershipArray;
1242	<	}
1242	>	}
1243		}
1244
1245		#ifdef IS_MPI
1246
1247	<	void SimSetup::mpiMolDivide( void ){
1205	<
1247	>	void SimSetup::mpiMolDivide(void){
1248		int i, j, k;
1249		int localMol, allMol;
1250		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1251
1252	<	mpiSim = new mpiSimulation( info );
1253	<
1252	>	mpiSim = new mpiSimulation(info);
1253	>
1254		globalIndex = mpiSim->divideLabor();
1255
1256		// set up the local variables
1257	<
1257	>
1258		mol2proc = mpiSim->getMolToProcMap();
1259		molCompType = mpiSim->getMolComponentType();
1260	<
1260	>
1261		allMol = 0;
1262		localMol = 0;
1263		local_atoms = 0;
#	Line 1225 | Line 1267 | void SimSetup::mpiMolDivide( void ){
1267		globalAtomIndex = 0;
1268
1269
1270	<	for( i=0; i<n_components; i++ ){
1271	<
1272	<	for( j=0; j<components_nmol[i]; j++ ){
1273	<
1274	<	if( mol2proc[allMol] == worldRank ){
1275	<
1276	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1277	<	local_bonds +=    comp_stamps[i]->getNBonds();
1236	<	local_bends +=    comp_stamps[i]->getNBends();
1237	<	local_torsions += comp_stamps[i]->getNTorsions();
1238	<	localMol++;
1270	>	for (i = 0; i < n_components; i++){
1271	>	for (j = 0; j < components_nmol[i]; j++){
1272	>	if (mol2proc[allMol] == worldRank){
1273	>	local_atoms += comp_stamps[i]->getNAtoms();
1274	>	local_bonds += comp_stamps[i]->getNBonds();
1275	>	local_bends += comp_stamps[i]->getNBends();
1276	>	local_torsions += comp_stamps[i]->getNTorsions();
1277	>	localMol++;
1278		}
1279	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1279	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1280		info[0].molMembershipArray[globalAtomIndex] = allMol;
1281		globalAtomIndex++;
1282		}
1283
1284	<	allMol++;
1284	>	allMol++;
1285		}
1286		}
1287		local_SRI = local_bonds + local_bends + local_torsions;
1288	<
1288	>
1289		info[0].n_atoms = mpiSim->getMyNlocal();
1290	<
1291	<	if( local_atoms != info[0].n_atoms ){
1292	<	sprintf( painCave.errMsg,
1293	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1294	<	" localAtom (%d) are not equal.\n",
1295	<	info[0].n_atoms,
1257	<	local_atoms );
1290	>
1291	>	if (local_atoms != info[0].n_atoms){
1292	>	sprintf(painCave.errMsg,
1293	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1294	>	"\tlocalAtom (%d) are not equal.\n",
1295	>	info[0].n_atoms, local_atoms);
1296		painCave.isFatal = 1;
1297		simError();
1298		}
#	Line 1265 | Line 1303 | void SimSetup::mpiMolDivide( void ){
1303		info[0].n_SRI = local_SRI;
1304		info[0].n_mol = localMol;
1305
1306	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1306	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1307		MPIcheckPoint();
1308		}
1309	<
1309	>
1310		#endif // is_mpi
1311
1312
1313	<	void SimSetup::makeSysArrays( void ){
1314	<	int i, j, k, l;
1313	>	void SimSetup::makeSysArrays(void){
1314	>
1315	>	#ifndef IS_MPI
1316	>	int k, j;
1317	>	#endif // is_mpi
1318	>	int i, l;
1319
1320		Atom** the_atoms;
1321		Molecule* the_molecules;
1322		Exclude** the_excludes;
1323
1324	<
1325	<	for(l=0; l<nInfo; l++){
1284	<
1324	>
1325	>	for (l = 0; l < nInfo; l++){
1326		// create the atom and short range interaction arrays
1327	<
1328	<	the_atoms = new Atom*[info[l].n_atoms];
1327	>
1328	>	the_atoms = new Atom * [info[l].n_atoms];
1329		the_molecules = new Molecule[info[l].n_mol];
1330		int molIndex;
1331
1332		// initialize the molecule's stampID's
1333	<
1333	>
1334		#ifdef IS_MPI
1335	<
1336	<
1335	>
1336	>
1337		molIndex = 0;
1338	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1339	<
1340	<	if(mol2proc[i] == worldRank ){
1341	<	the_molecules[molIndex].setStampID( molCompType[i] );
1342	<	the_molecules[molIndex].setMyIndex( molIndex );
1343	<	the_molecules[molIndex].setGlobalIndex( i );
1303	<	molIndex++;
1338	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1339	>	if (mol2proc[i] == worldRank){
1340	>	the_molecules[molIndex].setStampID(molCompType[i]);
1341	>	the_molecules[molIndex].setMyIndex(molIndex);
1342	>	the_molecules[molIndex].setGlobalIndex(i);
1343	>	molIndex++;
1344		}
1345		}
1346	<
1346	>
1347		#else // is_mpi
1348	<
1348	>
1349		molIndex = 0;
1350		globalAtomIndex = 0;
1351	<	for(i=0; i<n_components; i++){
1352	<	for(j=0; j<components_nmol[i]; j++ ){
1353	<	the_molecules[molIndex].setStampID( i );
1354	<	the_molecules[molIndex].setMyIndex( molIndex );
1355	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1356	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1357	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1358	<	globalAtomIndex++;
1359	<	}
1360	<	molIndex++;
1351	>	for (i = 0; i < n_components; i++){
1352	>	for (j = 0; j < components_nmol[i]; j++){
1353	>	the_molecules[molIndex].setStampID(i);
1354	>	the_molecules[molIndex].setMyIndex(molIndex);
1355	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1356	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1357	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1358	>	globalAtomIndex++;
1359	>	}
1360	>	molIndex++;
1361		}
1362		}
1363	<
1364	<
1363	>
1364	>
1365		#endif // is_mpi
1366
1367
1368	<	if( info[l].n_SRI ){
1329	<
1368	>	if (info[l].n_SRI){
1369		Exclude::createArray(info[l].n_SRI);
1370	<	the_excludes = new Exclude*[info[l].n_SRI];
1371	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1372	<	the_excludes[ex] = new Exclude(ex);
1370	>	the_excludes = new Exclude * [info[l].n_SRI];
1371	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1372	>	the_excludes[ex] = new Exclude(ex);
1373		}
1374		info[l].globalExcludes = new int;
1375		info[l].n_exclude = info[l].n_SRI;
1376		}
1377		else{
1378	<
1379	<	Exclude::createArray( 1 );
1341	<	the_excludes = new Exclude*;
1378	>	Exclude::createArray(1);
1379	>	the_excludes = new Exclude * ;
1380		the_excludes[0] = new Exclude(0);
1381	<	the_excludes[0]->setPair( 0,0 );
1381	>	the_excludes[0]->setPair(0, 0);
1382		info[l].globalExcludes = new int;
1383		info[l].globalExcludes[0] = 0;
1384		info[l].n_exclude = 0;
#	Line 1353 | Line 1391 | void SimSetup::makeSysArrays( void ){
1391		info[l].nGlobalExcludes = 0;
1392		info[l].excludes = the_excludes;
1393
1394	<	the_ff->setSimInfo( info );
1357	<
1394	>	the_ff->setSimInfo(info);
1395		}
1396		}
1397
1398	<	void SimSetup::makeIntegrator( void ){
1362	<
1398	>	void SimSetup::makeIntegrator(void){
1399		int k;
1400
1401	<	NVT<RealIntegrator>*  myNVT = NULL;
1402	<	NPTi<RealIntegrator>* myNPTi = NULL;
1403	<	NPTf<RealIntegrator>* myNPTf = NULL;
1404	<	NPTim<RealIntegrator>* myNPTim = NULL;
1405	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1406	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1407	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1408	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1409	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1410	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1411	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1412	<
1413	<	for(k=0; k<nInfo; k++){
1414	<
1415	<	switch( ensembleCase ){
1416	<
1417	<	case NVE_ENS:
1418	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1419	<	break;
1420	<
1421	<	case NVT_ENS:
1422	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1423	<	myNVT->setTargetTemp(globals->getTargetTemp());
1424	<
1425	<	if (globals->haveTauThermostat())
1426	<	myNVT->setTauThermostat(globals->getTauThermostat());
1427	<
1428	<	else {
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use the NVT\n"
1431	<	"    ensemble, you must set tauThermostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<	break;
1436	<
1437	<	case NPTi_ENS:
1438	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1439	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1440	<
1441	<	if (globals->haveTargetPressure())
1442	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1443	<	else {
1444	<	sprintf( painCave.errMsg,
1445	<	"SimSetup error: If you use a constant pressure\n"
1446	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1447	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1450	<
1451	<	if( globals->haveTauThermostat() )
1452	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1453	<	else{
1454	<	sprintf( painCave.errMsg,
1455	<	"SimSetup error: If you use an NPT\n"
1456	<	"    ensemble, you must set tauThermostat.\n");
1457	<	painCave.isFatal = 1;
1458	<	simError();
1459	<	}
1460	<
1461	<	if( globals->haveTauBarostat() )
1462	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1463	<	else{
1464	<	sprintf( painCave.errMsg,
1465	<	"SimSetup error: If you use an NPT\n"
1466	<	"    ensemble, you must set tauBarostat.\n");
1467	<	painCave.isFatal = 1;
1468	<	simError();
1469	<	}
1470	<	break;
1471	<
1472	<	case NPTf_ENS:
1473	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1474	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1475	<
1476	<	if (globals->haveTargetPressure())
1477	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1478	<	else {
1479	<	sprintf( painCave.errMsg,
1480	<	"SimSetup error: If you use a constant pressure\n"
1481	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1482	<	painCave.isFatal = 1;
1483	<	simError();
1484	<	}
1485	<
1486	<	if( globals->haveTauThermostat() )
1487	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1488	<	else{
1489	<	sprintf( painCave.errMsg,
1490	<	"SimSetup error: If you use an NPT\n"
1491	<	"    ensemble, you must set tauThermostat.\n");
1492	<	painCave.isFatal = 1;
1493	<	simError();
1494	<	}
1495	<
1496	<	if( globals->haveTauBarostat() )
1497	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1498	<	else{
1499	<	sprintf( painCave.errMsg,
1500	<	"SimSetup error: If you use an NPT\n"
1501	<	"    ensemble, you must set tauBarostat.\n");
1502	<	painCave.isFatal = 1;
1503	<	simError();
1504	<	}
1505	<	break;
1506	<
1507	<	case NPTim_ENS:
1508	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1509	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	<
1511	<	if (globals->haveTargetPressure())
1512	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	<	else {
1514	<	sprintf( painCave.errMsg,
1515	<	"SimSetup error: If you use a constant pressure\n"
1516	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	<	painCave.isFatal = 1;
1518	<	simError();
1519	<	}
1520	<
1521	<	if( globals->haveTauThermostat() )
1522	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	<	else{
1524	<	sprintf( painCave.errMsg,
1525	<	"SimSetup error: If you use an NPT\n"
1526	<	"    ensemble, you must set tauThermostat.\n");
1527	<	painCave.isFatal = 1;
1528	<	simError();
1529	<	}
1530	<
1531	<	if( globals->haveTauBarostat() )
1532	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	<	else{
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use an NPT\n"
1536	<	"    ensemble, you must set tauBarostat.\n");
1537	<	painCave.isFatal = 1;
1538	<	simError();
1539	<	}
1540	<	break;
1541	<
1542	<	case NPTfm_ENS:
1543	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1544	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1545	<
1546	<	if (globals->haveTargetPressure())
1547	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1548	<	else {
1549	<	sprintf( painCave.errMsg,
1550	<	"SimSetup error: If you use a constant pressure\n"
1551	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1552	<	painCave.isFatal = 1;
1553	<	simError();
1554	<	}
1555	<
1556	<	if( globals->haveTauThermostat() )
1557	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1558	<	else{
1559	<	sprintf( painCave.errMsg,
1560	<	"SimSetup error: If you use an NPT\n"
1561	<	"    ensemble, you must set tauThermostat.\n");
1562	<	painCave.isFatal = 1;
1563	<	simError();
1564	<	}
1565	<
1566	<	if( globals->haveTauBarostat() )
1567	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1568	<	else{
1569	<	sprintf( painCave.errMsg,
1570	<	"SimSetup error: If you use an NPT\n"
1571	<	"    ensemble, you must set tauBarostat.\n");
1572	<	painCave.isFatal = 1;
1573	<	simError();
1574	<	}
1575	<	break;
1576	<
1577	<	case NVEZCONS_ENS:
1578	<
1579	<
1544	<	//setup index of z-constraint molecules, z-constraint sampel time
1545	<	//and z-constraint force output name. These parameter should be known
1546	<	//before constructing the z-constraint integrator
1547	<	setupZConstraint();
1548	<
1549	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	<
1551	<	break;
1552	<
1553	<
1554	<	case NVTZCONS_ENS:
1555	<
1556	<	setupZConstraint();
1557	<
1558	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	<
1561	<	if (globals->haveTauThermostat())
1562	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	<
1564	<	else {
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use the NVT\n"
1567	<	"    ensemble, you must set tauThermostat.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1570	<	}
1571	<	break;
1572	<
1573	<	case NPTiZCONS_ENS:
1574	<
1575	<	setupZConstraint();
1576	<
1577	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	<
1580	<	if (globals->haveTargetPressure())
1581	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	<	else {
1583	<	sprintf( painCave.errMsg,
1584	<	"SimSetup error: If you use a constant pressure\n"
1585	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	<	painCave.isFatal = 1;
1587	<	simError();
1588	<	}
1589	<
1590	<	if( globals->haveTauThermostat() )
1591	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	<	else{
1593	<	sprintf( painCave.errMsg,
1594	<	"SimSetup error: If you use an NPT\n"
1595	<	"    ensemble, you must set tauThermostat.\n");
1596	<	painCave.isFatal = 1;
1597	<	simError();
1598	<	}
1599	<
1600	<	if( globals->haveTauBarostat() )
1601	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	<	else{
1603	<	sprintf( painCave.errMsg,
1604	<	"SimSetup error: If you use an NPT\n"
1605	<	"    ensemble, you must set tauBarostat.\n");
1606	<	painCave.isFatal = 1;
1607	<	simError();
1608	<	}
1609	<
1610	<	break;
1611	<
1612	<	case NPTfZCONS_ENS:
1613	<
1614	<	setupZConstraint();
1615	<
1616	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	<
1619	<	if (globals->haveTargetPressure())
1620	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	<	else {
1622	<	sprintf( painCave.errMsg,
1623	<	"SimSetup error: If you use a constant pressure\n"
1624	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	<	painCave.isFatal = 1;
1626	<	simError();
1627	<	}
1628	<
1629	<	if( globals->haveTauThermostat() )
1630	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	<	else{
1632	<	sprintf( painCave.errMsg,
1633	<	"SimSetup error: If you use an NPT\n"
1634	<	"    ensemble, you must set tauThermostat.\n");
1635	<	painCave.isFatal = 1;
1636	<	simError();
1637	<	}
1638	<
1639	<	if( globals->haveTauBarostat() )
1640	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	<	else{
1642	<	sprintf( painCave.errMsg,
1643	<	"SimSetup error: If you use an NPT\n"
1644	<	"    ensemble, you must set tauBarostat.\n");
1645	<	painCave.isFatal = 1;
1646	<	simError();
1647	<	}
1648	<
1649	<	break;
1650	<
1651	<	case NPTimZCONS_ENS:
1652	<
1653	<	setupZConstraint();
1654	<
1655	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	<
1658	<	if (globals->haveTargetPressure())
1659	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	<	else {
1661	<	sprintf( painCave.errMsg,
1662	<	"SimSetup error: If you use a constant pressure\n"
1663	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	<	painCave.isFatal = 1;
1665	<	simError();
1666	<	}
1667	<
1668	<	if( globals->haveTauThermostat() )
1669	<	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	<	else{
1671	<	sprintf( painCave.errMsg,
1672	<	"SimSetup error: If you use an NPT\n"
1673	<	"    ensemble, you must set tauThermostat.\n");
1674	<	painCave.isFatal = 1;
1675	<	simError();
1676	<	}
1677	<
1678	<	if( globals->haveTauBarostat() )
1679	<	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	<	else{
1681	<	sprintf( painCave.errMsg,
1682	<	"SimSetup error: If you use an NPT\n"
1683	<	"    ensemble, you must set tauBarostat.\n");
1684	<	painCave.isFatal = 1;
1685	<	simError();
1686	<	}
1687	<
1688	<	break;
1689	<
1690	<	case NPTfmZCONS_ENS:
1691	<
1692	<	setupZConstraint();
1693	<
1694	<	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	<	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	<
1697	<	if (globals->haveTargetPressure())
1698	<	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	<	else {
1700	<	sprintf( painCave.errMsg,
1701	<	"SimSetup error: If you use a constant pressure\n"
1702	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	<	painCave.isFatal = 1;
1704	<	simError();
1705	<	}
1706	<
1707	<	if( globals->haveTauThermostat() )
1708	<	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	<	else{
1710	<	sprintf( painCave.errMsg,
1711	<	"SimSetup error: If you use an NPT\n"
1712	<	"    ensemble, you must set tauThermostat.\n");
1713	<	painCave.isFatal = 1;
1714	<	simError();
1715	<	}
1716	<
1717	<	if( globals->haveTauBarostat() )
1718	<	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	<	else{
1720	<	sprintf( painCave.errMsg,
1721	<	"SimSetup error: If you use an NPT\n"
1722	<	"    ensemble, you must set tauBarostat.\n");
1723	<	painCave.isFatal = 1;
1724	<	simError();
1725	<	}
1726	<	break;
1727	<
1728	<
1729	<
1730	<	default:
1731	<	sprintf( painCave.errMsg,
1732	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733	<	painCave.isFatal = 1;
1734	<	simError();
1401	>	NVE<RealIntegrator>* myNVE = NULL;
1402	>	NVT<RealIntegrator>* myNVT = NULL;
1403	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1404	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1405	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1406	>
1407	>	for (k = 0; k < nInfo; k++){
1408	>	switch (ensembleCase){
1409	>	case NVE_ENS:
1410	>	if (globals->haveZconstraints()){
1411	>	setupZConstraint(info[k]);
1412	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1413	>	}
1414	>	else{
1415	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1416	>	}
1417	>
1418	>	info->the_integrator = myNVE;
1419	>	break;
1420	>
1421	>	case NVT_ENS:
1422	>	if (globals->haveZconstraints()){
1423	>	setupZConstraint(info[k]);
1424	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1425	>	}
1426	>	else
1427	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1428	>
1429	>	myNVT->setTargetTemp(globals->getTargetTemp());
1430	>
1431	>	if (globals->haveTauThermostat())
1432	>	myNVT->setTauThermostat(globals->getTauThermostat());
1433	>	else{
1434	>	sprintf(painCave.errMsg,
1435	>	"SimSetup error: If you use the NVT\n"
1436	>	"\tensemble, you must set tauThermostat.\n");
1437	>	painCave.isFatal = 1;
1438	>	simError();
1439	>	}
1440	>
1441	>	info->the_integrator = myNVT;
1442	>	break;
1443	>
1444	>	case NPTi_ENS:
1445	>	if (globals->haveZconstraints()){
1446	>	setupZConstraint(info[k]);
1447	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1448	>	}
1449	>	else
1450	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1451	>
1452	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1453	>
1454	>	if (globals->haveTargetPressure())
1455	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1456	>	else{
1457	>	sprintf(painCave.errMsg,
1458	>	"SimSetup error: If you use a constant pressure\n"
1459	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1460	>	painCave.isFatal = 1;
1461	>	simError();
1462	>	}
1463	>
1464	>	if (globals->haveTauThermostat())
1465	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1466	>	else{
1467	>	sprintf(painCave.errMsg,
1468	>	"SimSetup error: If you use an NPT\n"
1469	>	"\tensemble, you must set tauThermostat.\n");
1470	>	painCave.isFatal = 1;
1471	>	simError();
1472	>	}
1473	>
1474	>	if (globals->haveTauBarostat())
1475	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1476	>	else{
1477	>	sprintf(painCave.errMsg,
1478	>	"SimSetup error: If you use an NPT\n"
1479	>	"\tensemble, you must set tauBarostat.\n");
1480	>	painCave.isFatal = 1;
1481	>	simError();
1482	>	}
1483	>
1484	>	info->the_integrator = myNPTi;
1485	>	break;
1486	>
1487	>	case NPTf_ENS:
1488	>	if (globals->haveZconstraints()){
1489	>	setupZConstraint(info[k]);
1490	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1491	>	}
1492	>	else
1493	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1494	>
1495	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1496	>
1497	>	if (globals->haveTargetPressure())
1498	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1499	>	else{
1500	>	sprintf(painCave.errMsg,
1501	>	"SimSetup error: If you use a constant pressure\n"
1502	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505	>	}
1506	>
1507	>	if (globals->haveTauThermostat())
1508	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1509	>
1510	>	else{
1511	>	sprintf(painCave.errMsg,
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"\tensemble, you must set tauThermostat.\n");
1514	>	painCave.isFatal = 1;
1515	>	simError();
1516	>	}
1517	>
1518	>	if (globals->haveTauBarostat())
1519	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1520	>
1521	>	else{
1522	>	sprintf(painCave.errMsg,
1523	>	"SimSetup error: If you use an NPT\n"
1524	>	"\tensemble, you must set tauBarostat.\n");
1525	>	painCave.isFatal = 1;
1526	>	simError();
1527	>	}
1528	>
1529	>	info->the_integrator = myNPTf;
1530	>	break;
1531	>
1532	>	case NPTxyz_ENS:
1533	>	if (globals->haveZconstraints()){
1534	>	setupZConstraint(info[k]);
1535	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1536	>	}
1537	>	else
1538	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1539	>
1540	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1541	>
1542	>	if (globals->haveTargetPressure())
1543	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1544	>	else{
1545	>	sprintf(painCave.errMsg,
1546	>	"SimSetup error: If you use a constant pressure\n"
1547	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1548	>	painCave.isFatal = 1;
1549	>	simError();
1550	>	}
1551	>
1552	>	if (globals->haveTauThermostat())
1553	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1554	>	else{
1555	>	sprintf(painCave.errMsg,
1556	>	"SimSetup error: If you use an NPT\n"
1557	>	"\tensemble, you must set tauThermostat.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560	>	}
1561	>
1562	>	if (globals->haveTauBarostat())
1563	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1564	>	else{
1565	>	sprintf(painCave.errMsg,
1566	>	"SimSetup error: If you use an NPT\n"
1567	>	"\tensemble, you must set tauBarostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570	>	}
1571	>
1572	>	info->the_integrator = myNPTxyz;
1573	>	break;
1574	>
1575	>	default:
1576	>	sprintf(painCave.errMsg,
1577	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1578	>	painCave.isFatal = 1;
1579	>	simError();
1580		}
1581		}
1582		}
1583
1584	<	void SimSetup::initFortran( void ){
1740	<
1584	>	void SimSetup::initFortran(void){
1585		info[0].refreshSim();
1586	<
1587	<	if( !strcmp( info[0].mixingRule, "standard") ){
1588	<	the_ff->initForceField( LB_MIXING_RULE );
1586	>
1587	>	if (!strcmp(info[0].mixingRule, "standard")){
1588	>	the_ff->initForceField(LB_MIXING_RULE);
1589		}
1590	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1591	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1590	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1591	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1592		}
1593		else{
1594	<	sprintf( painCave.errMsg,
1595	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	<	info[0].mixingRule );
1594	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1595	>	info[0].mixingRule);
1596		painCave.isFatal = 1;
1597		simError();
1598		}
1599
1600
1601		#ifdef IS_MPI
1602	<	strcpy( checkPointMsg,
1760	<	"Successfully intialized the mixingRule for Fortran." );
1602	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1603		MPIcheckPoint();
1604		#endif // is_mpi
1605	+	}
1606
1607	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1608	+	int nZConstraints;
1609	+	ZconStamp** zconStamp;
1610	+
1611	+	if (globals->haveZconstraintTime()){
1612	+	//add sample time of z-constraint  into SimInfo's property list
1613	+	DoubleData* zconsTimeProp = new DoubleData();
1614	+	zconsTimeProp->setID(ZCONSTIME_ID);
1615	+	zconsTimeProp->setData(globals->getZconsTime());
1616	+	theInfo.addProperty(zconsTimeProp);
1617	+	}
1618	+	else{
1619	+	sprintf(painCave.errMsg,
1620	+	"ZConstraint error: If you use a ZConstraint,\n"
1621	+	"\tyou must set zconsTime.\n");
1622	+	painCave.isFatal = 1;
1623	+	simError();
1624	+	}
1625	+
1626	+	//push zconsTol into siminfo, if user does not specify
1627	+	//value for zconsTol, a default value will be used
1628	+	DoubleData* zconsTol = new DoubleData();
1629	+	zconsTol->setID(ZCONSTOL_ID);
1630	+	if (globals->haveZconsTol()){
1631	+	zconsTol->setData(globals->getZconsTol());
1632	+	}
1633	+	else{
1634	+	double defaultZConsTol = 0.01;
1635	+	sprintf(painCave.errMsg,
1636	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1637	+	"\tOOPSE will use a default value of %f.\n"
1638	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1639	+	defaultZConsTol);
1640	+	painCave.isFatal = 0;
1641	+	simError();
1642	+
1643	+	zconsTol->setData(defaultZConsTol);
1644	+	}
1645	+	theInfo.addProperty(zconsTol);
1646	+
1647	+	//set Force Subtraction Policy
1648	+	StringData* zconsForcePolicy = new StringData();
1649	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1650	+
1651	+	if (globals->haveZconsForcePolicy()){
1652	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1653	+	}
1654	+	else{
1655	+	sprintf(painCave.errMsg,
1656	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1657	+	"\tOOPSE will use PolicyByMass.\n"
1658	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1659	+	painCave.isFatal = 0;
1660	+	simError();
1661	+	zconsForcePolicy->setData("BYMASS");
1662	+	}
1663	+
1664	+	theInfo.addProperty(zconsForcePolicy);
1665	+
1666	+	//Determine the name of ouput file and add it into SimInfo's property list
1667	+	//Be careful, do not use inFileName, since it is a pointer which
1668	+	//point to a string at master node, and slave nodes do not contain that string
1669	+
1670	+	string zconsOutput(theInfo.finalName);
1671	+
1672	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1673	+
1674	+	StringData* zconsFilename = new StringData();
1675	+	zconsFilename->setID(ZCONSFILENAME_ID);
1676	+	zconsFilename->setData(zconsOutput);
1677	+
1678	+	theInfo.addProperty(zconsFilename);
1679	+
1680	+	//setup index, pos and other parameters of z-constraint molecules
1681	+	nZConstraints = globals->getNzConstraints();
1682	+	theInfo.nZconstraints = nZConstraints;
1683	+
1684	+	zconStamp = globals->getZconStamp();
1685	+	ZConsParaItem tempParaItem;
1686	+
1687	+	ZConsParaData* zconsParaData = new ZConsParaData();
1688	+	zconsParaData->setID(ZCONSPARADATA_ID);
1689	+
1690	+	for (int i = 0; i < nZConstraints; i++){
1691	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1692	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1693	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1694	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1695	+
1696	+	zconsParaData->addItem(tempParaItem);
1697	+	}
1698	+
1699	+	//check the uniqueness of index
1700	+	if(!zconsParaData->isIndexUnique()){
1701	+	sprintf(painCave.errMsg,
1702	+	"ZConstraint Error: molIndex is not unique!\n");
1703	+	painCave.isFatal = 1;
1704	+	simError();
1705	+	}
1706	+
1707	+	//sort the parameters by index of molecules
1708	+	zconsParaData->sortByIndex();
1709	+
1710	+	//push data into siminfo, therefore, we can retrieve later
1711	+	theInfo.addProperty(zconsParaData);
1712		}
1713
1714	<	void SimSetup::setupZConstraint()
1767	<	{
1768	<	int k;
1714	>	void SimSetup::makeMinimizer(){
1715
1716	<	for(k=0; k<nInfo; k++){
1717	<
1718	<	if(globals->haveZConsTime()){
1719	<
1720	<	//add sample time of z-constraint  into SimInfo's property list
1721	<	DoubleData* zconsTimeProp = new DoubleData();
1722	<	zconsTimeProp->setID("zconstime");
1723	<	zconsTimeProp->setData(globals->getZConsTime());
1724	<	info[k].addProperty(zconsTimeProp);
1716	>	OOPSEMinimizerBase* myOOPSEMinimizerBase;
1717	>	ObjFunctor1 * objFunc;
1718	>	OutputFunctor* outputFunc;
1719	>	ConcreteNLModel1* nlp;
1720	>	MinimizerParameterSet* param;
1721	>	ConjugateMinimizerBase* minimizer;
1722	>	int dim;
1723	>
1724	>	for (int i = 0; i < nInfo; i++){
1725	>	//creat
1726	>	myOOPSEMinimizerBase = new OOPSEMinimizerBase(&(info[i]), the_ff);
1727	>
1728	>	//creat the object functor;
1729	>	objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase>
1730	>	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient);
1731	>
1732	>	//creat output functor;
1733	>	outputFunc =  new ClassMemOutputFunctor<OOPSEMinimizerBase>
1734	>	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::output);
1735	>
1736	>	//creat nonlinear model
1737	>	dim = myOOPSEMinimizerBase->getDim();
1738	>	nlp = new ConcreteNLModel1(dim, objFunc);
1739	>
1740	>	//prepare parameter set for minimizer
1741	>	param = new MinimizerParameterSet();
1742	>	param->setDefaultParameter();
1743	>
1744	>	if (globals->haveMinimizer()){
1745	>	param->setFTol(globals->getMinFTol());
1746		}
1747	<	else{
1748	<	sprintf( painCave.errMsg,
1749	<	"ZConstraint error: If you use an ZConstraint\n"
1783	<	" , you must set sample time.\n");
1784	<	painCave.isFatal = 1;
1785	<	simError();
1747	>
1748	>	if (globals->haveMinGTol()){
1749	>	param->setGTol(globals->getMinGTol());
1750		}
1751	<
1752	<	if(globals->haveIndexOfAllZConsMols()){
1753	<
1790	<	//add index of z-constraint molecules into SimInfo's property list
1791	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792	<
1793	<	//sort the index
1794	<	sort(tempIndex.begin(), tempIndex.end());
1795	<
1796	<	IndexData* zconsIndex = new IndexData();
1797	<	zconsIndex->setID("zconsindex");
1798	<	zconsIndex->setIndexData(tempIndex);
1799	<	info[k].addProperty(zconsIndex);
1751	>
1752	>	if (globals->haveMinMaxIter()){
1753	>	param->setMaxIteration(globals->getMinMaxIter());
1754		}
1755	<	else{
1756	<	sprintf( painCave.errMsg,
1757	<	"SimSetup error: If you use an ZConstraint\n"
1804	<	" , you must set index of z-constraint molecules.\n");
1805	<	painCave.isFatal = 1;
1806	<	simError();
1807	<
1755	>
1756	>	if (globals->haveMinWriteFrq()){
1757	>	param->setMaxIteration(globals->getMinMaxIter());
1758		}
1759	+
1760	+	if (globals->haveMinWriteFrq()){
1761	+	param->setWriteFrq(globals->getMinWriteFrq());
1762	+	}
1763
1764	<	//Determine the name of ouput file and add it into SimInfo's property list
1765	<	//Be careful, do not use inFileName, since it is a pointer which
1766	<	//point to a string at master node, and slave nodes do not contain that string
1764	>	if (globals->haveMinResetFrq()){
1765	>	param->setResetFrq(globals->getMinResetFrq());
1766	>	}
1767	>
1768	>	if (globals->haveMinLSMaxIter()){
1769	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1770	>	}
1771	>
1772	>	if (globals->haveMinLSTol()){
1773	>	param->setLineSearchTol(globals->getMinLSTol());
1774	>	}
1775
1776	<	string zconsOutput(info[k].finalName);
1777	<
1778	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1779	<
1780	<	StringData* zconsFilename = new StringData();
1781	<	zconsFilename->setID("zconsfilename");
1782	<	zconsFilename->setData(zconsOutput);
1783	<
1822	<	info[k].addProperty(zconsFilename);
1776	>	//creat the minimizer
1777	>	minimizer = new PRCGMinimizer(nlp, param);
1778	>	minimizer->setLineSearchStrategy(nlp, GoldenSection);
1779	>	minimizer->setOutputFunctor(outputFunc);
1780	>
1781	>	//store the minimizer into simInfo
1782	>	info[i].the_minimizer = minimizer;
1783	>	info[i].has_minimizer = true;
1784		}
1785	+
1786		}

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