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root/group/branches/new_design/OOPSE-3.0/src/constraints/ZConstraint.cpp

Comparing branches/new_design/OOPSE-3.0/src/constraints/ZConstraint.cpp (file contents):
Revision 1694, Thu Oct 28 22:34:02 2004 UTC vs.
Revision 1695 by tim, Mon Nov 1 22:52:57 2004 UTC

#	Line 1 | Line 1
1	<	#include "integrators/Integrator.hpp"
2	<	#include "utils/simError.h"
3	<	#include <math.h>
4	<
5	<	const double INFINITE_TIME = 10e30;
6	<	template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo,
7	<	ForceFields* the_ff): T(theInfo, the_ff),
8	<	fzOut(NULL),
9	<	curZconsTime(0),
10	<	forcePolicy(NULL),
11	<	usingSMD(false),
12	<	hasZConsGap(false){
13	<	//get properties from SimInfo
14	<	GenericData* data;
15	<	ZConsParaData* zConsParaData;
16	<	DoubleGenericData* sampleTime;
17	<	DoubleGenericData* tolerance;
18	<	DoubleGenericData* gap;
19	<	DoubleGenericData* fixtime;
20	<	StringGenericData* policy;
21	<	StringGenericData* filename;
22	<	IntGenericData* smdFlag;
23	<	double COM[3];
24	<
25	<	//by default, the direction of constraint is z
26	<	// 0 --> x
27	<	// 1 --> y
28	<	// 2 --> z
29	<	whichDirection = 2;
30	<
31	<	//estimate the force constant of harmonical potential
32	<	double Kb = 1.986E-3 ; //in kcal/K
33	<
34	<	double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /
35	<	2;
36	<	zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox);
37	<
38	<	//creat force Subtraction policy
39	<	data = info->getProperty(ZCONSFORCEPOLICY_ID);
40	<	if (!data){
41	<	sprintf(painCave.errMsg,
42	<	"ZConstraint Warning: User does not set force Subtraction policy, "
43	<	"PolicyByMass is used\n");
44	<	painCave.isFatal = 0;
45	<	simError();
46	<
47	<	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
48	<	}
49	<	else{
50	<	policy = dynamic_cast<StringGenericData*>(data);
51	<
52	<	if (!policy){
53	<	sprintf(painCave.errMsg,
54	<	"ZConstraint Error: Convertion from GenericData to StringGenericData failure, "
55	<	"PolicyByMass is used\n");
56	<	painCave.isFatal = 0;
57	<	simError();
58	<
59	<	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
60	<	}
61	<	else{
62	<	if (policy->getData() == "BYNUMBER")
63	<	forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this);
64	<	else if (policy->getData() == "BYMASS")
65	<	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
66	<	else{
67	<	sprintf(painCave.errMsg,
68	<	"ZConstraint Warning: unknown force Subtraction policy, "
69	<	"PolicyByMass is used\n");
70	<	painCave.isFatal = 0;
71	<	simError();
72	<	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
73	<	}
74	<	}
75	<	}
76	<
77	<
78	<	//retrieve sample time of z-contraint
79	<	data = info->getProperty(ZCONSTIME_ID);
80	<
81	<	if (!data){
82	<	sprintf(painCave.errMsg,
83	<	"ZConstraint error: If you use an ZConstraint\n"
84	<	" , you must set sample time.\n");
85	<	painCave.isFatal = 1;
86	<	simError();
87	<	}
88	<	else{
89	<	sampleTime = dynamic_cast<DoubleGenericData*>(data);
90	<
91	<	if (!sampleTime){
92	<	sprintf(painCave.errMsg,
93	<	"ZConstraint error: Can not get property from SimInfo\n");
94	<	painCave.isFatal = 1;
95	<	simError();
96	<	}
97	<	else{
98	<	this->zconsTime = sampleTime->getData();
99	<	}
100	<	}
101	<
102	<	//retrieve output filename of z force
103	<	data = info->getProperty(ZCONSFILENAME_ID);
104	<	if (!data){
105	<	sprintf(painCave.errMsg,
106	<	"ZConstraint error: If you use an ZConstraint\n"
107	<	" , you must set output filename of z-force.\n");
108	<	painCave.isFatal = 1;
109	<	simError();
110	<	}
111	<	else{
112	<	filename = dynamic_cast<StringGenericData*>(data);
113	<
114	<	if (!filename){
115	<	sprintf(painCave.errMsg,
116	<	"ZConstraint error: Can not get property from SimInfo\n");
117	<	painCave.isFatal = 1;
118	<	simError();
119	<	}
120	<	else{
121	<	this->zconsOutput = filename->getData();
122	<	}
123	<	}
124	<
125	<	//retrieve tolerance for z-constraint molecuels
126	<	data = info->getProperty(ZCONSTOL_ID);
127	<
128	<	if (!data){
129	<	sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n");
130	<	painCave.isFatal = 1;
131	<	simError();
132	<	}
133	<	else{
134	<	tolerance = dynamic_cast<DoubleGenericData*>(data);
135	<
136	<	if (!tolerance){
137	<	sprintf(painCave.errMsg,
138	<	"ZConstraint error: Can not get property from SimInfo\n");
139	<	painCave.isFatal = 1;
140	<	simError();
141	<	}
142	<	else{
143	<	this->zconsTol = tolerance->getData();
144	<	}
145	<	}
146	<
147	<	//quick hack here
148	<	data = info->getProperty(ZCONSGAP_ID);
149	<
150	<	if (data){
151	<	gap = dynamic_cast<DoubleGenericData*>(data);
152	<
153	<	if (!gap){
154	<	sprintf(painCave.errMsg,
155	<	"ZConstraint error: Can not get property from SimInfo\n");
156	<	painCave.isFatal = 1;
157	<	simError();
158	<	}
159	<	else{
160	<	this->hasZConsGap = true;
161	<	this->zconsGap = gap->getData();
162	<	}
163	<	}
164	<
165	<
166	<
167	<	data = info->getProperty(ZCONSFIXTIME_ID);
168	<
169	<	if (data){
170	<	fixtime = dynamic_cast<DoubleGenericData*>(data);
171	<	if (!fixtime){
172	<	sprintf(painCave.errMsg,
173	<	"ZConstraint error: Can not get zconsFixTime from SimInfo\n");
174	<	painCave.isFatal = 1;
175	<	simError();
176	<	}
177	<	else{
178	<	this->zconsFixTime = fixtime->getData();
179	<	}
180	<	}
181	<	else if(hasZConsGap){
182	<	sprintf(painCave.errMsg,
183	<	"ZConstraint error: must set fixtime if already set zconsGap\n");
184	<	painCave.isFatal = 1;
185	<	simError();
186	<	}
187	<
188	<
189	<
190	<	data = info->getProperty(ZCONSUSINGSMD_ID);
191	<
192	<	if (data){
193	<	smdFlag = dynamic_cast<IntGenericData*>(data);
194	<
195	<	if (!smdFlag){
196	<	sprintf(painCave.errMsg,
197	<	"ZConstraint error: Can not get property from SimInfo\n");
198	<	painCave.isFatal = 1;
199	<	simError();
200	<	}
201	<	else{
202	<	this->usingSMD= smdFlag->getData() ? true : false;
203	<	}
204	<
205	<	}
206	<
207	<
208	<
209	<	//retrieve index of z-constraint molecules
210	<	data = info->getProperty(ZCONSPARADATA_ID);
211	<	if (!data){
212	<	sprintf(painCave.errMsg,
213	<	"ZConstraint error: If you use an ZConstraint\n"
214	<	" , you must set index of z-constraint molecules.\n");
215	<	painCave.isFatal = 1;
216	<	simError();
217	<	}
218	<	else{
219	<	zConsParaData = dynamic_cast<ZConsParaData*>(data);
220	<
221	<	if (!zConsParaData){
222	<	sprintf(painCave.errMsg,
223	<	"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
224	<	painCave.isFatal = 1;
225	<	simError();
226	<	}
227	<	else{
228	<	parameters = zConsParaData->getData();
229	<
230	<	//check the range of zconsIndex
231	<	//and the minimum value of index is the first one (we already sorted the data)
232	<	//the maximum value of index is the last one
233	<
234	<	int maxIndex;
235	<	int minIndex;
236	<	int totalNumMol;
237	<
238	<	minIndex = (*parameters)[0].zconsIndex;
239	<	if (minIndex < 0){
240	<	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
241	<	painCave.isFatal = 1;
242	<	simError();
243	<	}
244	<
245	<	maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
246	<
247	<	#ifndef IS_MPI
248	<	totalNumMol = nMols;
249	<	#else
250	<	totalNumMol = mpiSim->getNMolGlobal();
251	<	#endif
252	<
253	<	if (maxIndex > totalNumMol - 1){
254	<	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
255	<	painCave.isFatal = 1;
256	<	simError();
257	<	}
258	<
259	<	//if user does not specify the zpos for the zconstraint molecule
260	<	//its initial z coordinate  will be used as default
261	<	for (int i = 0; i < (int) (parameters->size()); i++){
262	<	if (!(*parameters)[i].havingZPos){
263	<	#ifndef IS_MPI
264	<	for (int j = 0; j < nMols; j++){
265	<	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
266	<	molecules[j].getCOM(COM);
267	<	break;
268	<	}
269	<	}
270	<	#else
271	<	//query which processor current zconstraint molecule belongs to
272	<	int* MolToProcMap;
273	<	int whichNode;
274	<
275	<	MolToProcMap = mpiSim->getMolToProcMap();
276	<	whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
277	<
278	<	//broadcast the zpos of current z-contraint molecule
279	<	//the node which contain this
280	<
281	<	if (worldRank == whichNode){
282	<	for (int j = 0; j < nMols; j++)
283	<	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
284	<	molecules[j].getCOM(COM);
285	<	break;
286	<	}
287	<	}
288	<
289	<	MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode,
290	<	MPI_COMM_WORLD);
291	<	#endif
292	<
293	<	(*parameters)[i].zPos = COM[whichDirection];
294	<
295	<	sprintf(painCave.errMsg,
296	<	"ZConstraint warning: Does not specify zpos for z-constraint molecule "
297	<	"initial z coornidate will be used \n");
298	<	painCave.isFatal = 0;
299	<	simError();
300	<	}
301	<	}
302	<	}//end if (!zConsParaData)
303	<
304	<	}//end  if (!data)
305	<
306	<	//
307	<	#ifdef IS_MPI
308	<	update();
309	<	#else
310	<	int searchResult;
311	<
312	<	for (int i = 0; i < nMols; i++){
313	<	searchResult = isZConstraintMol(&molecules[i]);
314	<
315	<	if (searchResult > -1){
316	<	zconsMols.push_back(&molecules[i]);
317	<	massOfZConsMols.push_back(molecules[i].getTotalMass());
318	<
319	<	zPos.push_back((*parameters)[searchResult].zPos);
320	<	kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
321	<
322	<	if(usingSMD)
323	<	cantVel.push_back((*parameters)[searchResult].cantVel);
324	<
325	<	}
326	<	else{
327	<	unconsMols.push_back(&molecules[i]);
328	<	massOfUnconsMols.push_back(molecules[i].getTotalMass());
329	<	}
330	<	}
331	<
332	<	fz.resize(zconsMols.size());
333	<	curZPos.resize(zconsMols.size());
334	<	indexOfZConsMols.resize(zconsMols.size());
335	<
336	<	//determine the states of z-constraint molecules
337	<	for (size_t i = 0; i < zconsMols.size(); i++){
338	<	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
339	<
340	<	zconsMols[i]->getCOM(COM);
341	<
342	<	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
343	<	states.push_back(zcsFixed);
344	<
345	<	if (hasZConsGap)
346	<	endFixTime.push_back(info->getTime() + zconsFixTime);
347	<	}
348	<	else{
349	<	states.push_back(zcsMoving);
350	<
351	<	if (hasZConsGap)
352	<	endFixTime.push_back(INFINITE_TIME);
353	<	}
354	<
355	<	if(usingSMD)
356	<	cantPos.push_back(COM[whichDirection]);
357	<	}
358	<
359	<	if(usingSMD)
360	<	prevCantPos = cantPos;
361	<	#endif
362	<
363	<
364	<	//get total masss of unconstraint molecules
365	<	double totalMassOfUncons_local;
366	<	totalMassOfUncons_local = 0;
367	<
368	<	for (size_t i = 0; i < unconsMols.size(); i++)
369	<	totalMassOfUncons_local += unconsMols[i]->getTotalMass();
370	<
371	<	#ifndef IS_MPI
372	<	totalMassOfUncons = totalMassOfUncons_local;
373	<	#else
374	<	MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,
375	<	MPI_SUM, MPI_COMM_WORLD);
376	<	#endif
377	<
378	<	//get total number of unconstrained atoms
379	<	int nUnconsAtoms_local;
380	<	nUnconsAtoms_local = 0;
381	<	for (int i = 0; i < (int) (unconsMols.size()); i++)
382	<	nUnconsAtoms_local += unconsMols[i]->getNAtoms();
383	<
384	<	#ifndef IS_MPI
385	<	totNumOfUnconsAtoms = nUnconsAtoms_local;
386	<	#else
387	<	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM,
388	<	MPI_COMM_WORLD);
389	<	#endif
390	<
391	<	forcePolicy->update();
392	<	}
393	<
394	<	template<typename T> ZConstraint<T>::~ZConstraint(){
395	<
396	<	if (fzOut){
397	<	delete fzOut;
398	<	}
399	<
400	<	if (forcePolicy){
401	<	delete forcePolicy;
402	<	}
403	<	}
404	<
405	<
406	<	/**
407	<	*
408	<	*/
409	<
410	<	#ifdef IS_MPI
411	<	template<typename T> void ZConstraint<T>::update(){
412	<	double COM[3];
413	<	int index;
414	<
415	<	zconsMols.clear();
416	<	massOfZConsMols.clear();
417	<	zPos.clear();
418	<	kz.clear();
419	<	cantPos.clear();
420	<	cantVel.clear();
421	<
422	<	unconsMols.clear();
423	<	massOfUnconsMols.clear();
424	<
425	<
426	<	//creat zconsMol and unconsMol lists
427	<	for (int i = 0; i < nMols; i++){
428	<	index = isZConstraintMol(&molecules[i]);
429	<
430	<	if (index > -1){
431	<	zconsMols.push_back(&molecules[i]);
432	<	zPos.push_back((*parameters)[index].zPos);
433	<	kz.push_back((*parameters)[index].kRatio * zForceConst);
434	<	massOfZConsMols.push_back(molecules[i].getTotalMass());
435	<
436	<	if(usingSMD)
437	<	cantVel.push_back((*parameters)[index].cantVel);
438	<
439	<	}
440	<	else{
441	<	unconsMols.push_back(&molecules[i]);
442	<	massOfUnconsMols.push_back(molecules[i].getTotalMass());
443	<	}
444	<	}
445	<
446	<	fz.resize(zconsMols.size());
447	<	curZPos.resize(zconsMols.size());
448	<	indexOfZConsMols.resize(zconsMols.size());
449	<
450	<	for (size_t i = 0; i < zconsMols.size(); i++){
451	<	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
452	<	}
453	<
454	<	//determine the states of z-constraint molecules
455	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
456	<
457	<	zconsMols[i]->getCOM(COM);
458	<
459	<	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
460	<	states.push_back(zcsFixed);
461	<
462	<	if (hasZConsGap)
463	<	endFixTime.push_back(info->getTime() + zconsFixTime);
464	<	}
465	<	else{
466	<	states.push_back(zcsMoving);
467	<
468	<	if (hasZConsGap)
469	<	endFixTime.push_back(INFINITE_TIME);
470	<	}
471	<
472	<	if(usingSMD)
473	<	cantPos.push_back(COM[whichDirection]);
474	<	}
475	<
476	<	if(usingSMD)
477	<	prevCantPos = cantPos;
478	<
479	<	forcePolicy->update();
480	<	}
481	<
482	<	#endif
483	<
484	<	/**
485	<	*  Function Name: isZConstraintMol
486	<	*  Parameter
487	<	*    Molecule* mol
488	<	*  Return value:
489	<	*    -1, if the molecule is not z-constraint molecule,
490	<	*    other non-negative values, its index in indexOfAllZConsMols vector
491	<	*/
492	<
493	<	template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){
494	<	int index;
495	<	int low;
496	<	int high;
497	<	int mid;
498	<
499	<	index = mol->getGlobalIndex();
500	<
501	<	low = 0;
502	<	high = parameters->size() - 1;
503	<
504	<	//Binary Search (we have sorted the array)
505	<	while (low <= high){
506	<	mid = (low + high) / 2;
507	<	if ((*parameters)[mid].zconsIndex == index)
508	<	return mid;
509	<	else if ((*parameters)[mid].zconsIndex > index)
510	<	high = mid - 1;
511	<	else
512	<	low = mid + 1;
513	<	}
514	<
515	<	return -1;
516	<	}
517	<
518	<	template<typename T> void ZConstraint<T>::integrate(){
519	<	// creat zconsWriter
520	<	fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
521	<
522	<	if (!fzOut){
523	<	sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<
528	<	//zero out the velocities of center of mass of unconstrained molecules
529	<	//and the velocities of center of mass of every single z-constrained molecueles
530	<	zeroOutVel();
531	<
532	<	curZconsTime = zconsTime + info->getTime();
533	<
534	<	T::integrate();
535	<	}
536	<
537	<	template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
538	<	double zsys;
539	<	double COM[3];
540	<	double force[3];
541	<	double zSysCOMVel;
542	<
543	<	T::calcForce(calcPot, calcStress);
544	<
545	<
546	<	if (hasZConsGap){
547	<	updateZPos();
548	<	}
549	<
550	<	if (checkZConsState()){
551	<	zeroOutVel();
552	<	forcePolicy->update();
553	<	}
554	<
555	<	zsys = calcZSys();
556	<	zSysCOMVel = calcSysCOMVel();
557	<	#ifdef IS_MPI
558	<	if (worldRank == 0){
559	<	#endif
560	<
561	<	#ifdef IS_MPI
562	<	}
563	<	#endif
564	<
565	<	//do zconstraint force;
566	<	if (haveFixedZMols()){
567	<	this->doZconstraintForce();
568	<	}
569	<
570	<	//use external force to move the molecules to the specified positions
571	<	if (haveMovingZMols()){
572	<	if (usingSMD)
573	<	this->doHarmonic(cantPos);
574	<	else
575	<	this->doHarmonic(zPos);
576	<	}
577	<
578	<	//write out forces and current positions of z-constraint molecules
579	<	if (info->getTime() >= curZconsTime){
580	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
581	<	zconsMols[i]->getCOM(COM);
582	<	curZPos[i] = COM[whichDirection];
583	<
584	<	//if the z-constraint molecule is still moving, just record its force
585	<	if (states[i] == zcsMoving){
586	<	fz[i] = 0;
587	<	Atom** movingZAtoms;
588	<	movingZAtoms = zconsMols[i]->getMyAtoms();
589	<	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
590	<	movingZAtoms[j]->getFrc(force);
591	<	fz[i] += force[whichDirection];
592	<	}
593	<	}
594	<	}
595	<	fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],
596	<	&curZPos[0], &zPos[0]);
597	<	curZconsTime += zconsTime;
598	<	}
599	<
600	<	zSysCOMVel = calcSysCOMVel();
601	<	#ifdef IS_MPI
602	<	if (worldRank == 0){
603	<	#endif
604	<	#ifdef IS_MPI
605	<	}
606	<	#endif
607	<	}
608	<
609	<
610	<	template<typename T> double ZConstraint<T>::calcZSys(){
611	<	//calculate reference z coordinate for z-constraint molecules
612	<	double totalMass_local;
613	<	double totalMass;
614	<	double totalMZ_local;
615	<	double totalMZ;
616	<	double massOfCurMol;
617	<	double COM[3];
618	<
619	<	totalMass_local = 0;
620	<	totalMZ_local = 0;
621	<
622	<	for (int i = 0; i < nMols; i++){
623	<	massOfCurMol = molecules[i].getTotalMass();
624	<	molecules[i].getCOM(COM);
625	<
626	<	totalMass_local += massOfCurMol;
627	<	totalMZ_local += massOfCurMol * COM[whichDirection];
628	<	}
629	<
630	<
631	<	#ifdef IS_MPI
632	<	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,
633	<	MPI_COMM_WORLD);
634	<	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
635	<	#else
636	<	totalMass = totalMass_local;
637	<	totalMZ = totalMZ_local;
638	<	#endif
639	<
640	<	double zsys;
641	<	zsys = totalMZ / totalMass;
642	<
643	<	return zsys;
644	<	}
645	<
646	<	template<typename T> void ZConstraint<T>::thermalize(void){
647	<	T::thermalize();
648	<	zeroOutVel();
649	<	}
650	<
651	<	template<typename T> void ZConstraint<T>::zeroOutVel(){
652	<	Atom** fixedZAtoms;
653	<	double COMvel[3];
654	<	double vel[3];
655	<	double zSysCOMVel;
656	<
657	<	//zero out the velocities of center of mass of fixed z-constrained molecules
658	<
659	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
660	<	if (states[i] == zcsFixed){
661	<	zconsMols[i]->getCOMvel(COMvel);
662	<	//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663	<
664	<	fixedZAtoms = zconsMols[i]->getMyAtoms();
665	<
666	<	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
667	<	fixedZAtoms[j]->getVel(vel);
668	<	vel[whichDirection] -= COMvel[whichDirection];
669	<	fixedZAtoms[j]->setVel(vel);
670	<	}
671	<
672	<	zconsMols[i]->getCOMvel(COMvel);
673	<	}
674	<	}
675	<
676	<	zSysCOMVel = calcSysCOMVel();
677	<	#ifdef IS_MPI
678	<	if (worldRank == 0){
679	<	#endif
680	<	#ifdef IS_MPI
681	<	}
682	<	#endif
683	<
684	<	// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
685	<	double MVzOfMovingMols_local;
686	<	double MVzOfMovingMols;
687	<	double totalMassOfMovingZMols_local;
688	<	double totalMassOfMovingZMols;
689	<
690	<	MVzOfMovingMols_local = 0;
691	<	totalMassOfMovingZMols_local = 0;
692	<
693	<	for (int i = 0; i < (int) (unconsMols.size()); i++){
694	<	unconsMols[i]->getCOMvel(COMvel);
695	<	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
696	<	}
697	<
698	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
699	<	if (states[i] == zcsMoving){
700	<	zconsMols[i]->getCOMvel(COMvel);
701	<	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
702	<	totalMassOfMovingZMols_local += massOfZConsMols[i];
703	<	}
704	<	}
705	<
706	<	#ifndef IS_MPI
707	<	MVzOfMovingMols = MVzOfMovingMols_local;
708	<	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
709	<	#else
710	<	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
711	<	MPI_SUM, MPI_COMM_WORLD);
712	<	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
713	<	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
714	<	#endif
715	<
716	<	double vzOfMovingMols;
717	<	vzOfMovingMols = MVzOfMovingMols /
718	<	(totalMassOfUncons + totalMassOfMovingZMols);
719	<
720	<	//modify the velocites of unconstrained molecules
721	<	Atom** unconsAtoms;
722	<	for (int i = 0; i < (int) (unconsMols.size()); i++){
723	<	unconsAtoms = unconsMols[i]->getMyAtoms();
724	<	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
725	<	unconsAtoms[j]->getVel(vel);
726	<	vel[whichDirection] -= vzOfMovingMols;
727	<	unconsAtoms[j]->setVel(vel);
728	<	}
729	<	}
730	<
731	<	//modify the velocities of moving z-constrained molecuels
732	<	Atom** movingZAtoms;
733	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
734	<	if (states[i] == zcsMoving){
735	<	movingZAtoms = zconsMols[i]->getMyAtoms();
736	<	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
737	<	movingZAtoms[j]->getVel(vel);
738	<	vel[whichDirection] -= vzOfMovingMols;
739	<	movingZAtoms[j]->setVel(vel);
740	<	}
741	<	}
742	<	}
743	<
744	<
745	<	zSysCOMVel = calcSysCOMVel();
746	<	#ifdef IS_MPI
747	<	if (worldRank == 0){
748	<	#endif
749	<	#ifdef IS_MPI
750	<	}
751	<	#endif
752	<	}
753	<
754	<
755	<	template<typename T> void ZConstraint<T>::doZconstraintForce(){
756	<	Atom** zconsAtoms;
757	<	double totalFZ;
758	<	double totalFZ_local;
759	<	double COM[3];
760	<	double force[3];
761	<
762	<	//constrain the molecules which do not reach the specified positions
763	<
764	<	//Zero Out the force of z-contrained molecules
765	<	totalFZ_local = 0;
766	<
767	<	//calculate the total z-contrained force of fixed z-contrained molecules
768	<
769	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
770	<	if (states[i] == zcsFixed){
771	<	zconsMols[i]->getCOM(COM);
772	<	zconsAtoms = zconsMols[i]->getMyAtoms();
773	<
774	<	fz[i] = 0;
775	<	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
776	<	zconsAtoms[j]->getFrc(force);
777	<	fz[i] += force[whichDirection];
778	<	}
779	<	totalFZ_local += fz[i];
780	<
781	<	}
782	<	}
783	<
784	<	//calculate total z-constraint force
785	<	#ifdef IS_MPI
786	<	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
787	<	#else
788	<	totalFZ = totalFZ_local;
789	<	#endif
790	<
791	<
792	<	// apply negative to fixed z-constrained molecues;
793	<	force[0] = 0;
794	<	force[1] = 0;
795	<	force[2] = 0;
796	<
797	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
798	<	if (states[i] == zcsFixed){
799	<	int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
800	<	zconsAtoms = zconsMols[i]->getMyAtoms();
801	<
802	<	for (int j = 0; j < nAtomOfCurZConsMol; j++){
803	<	//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
804	<	force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],
805	<	zconsAtoms[j],
806	<	fz[i]);
807	<	zconsAtoms[j]->addFrc(force);
808	<	}
809	<	}
810	<	}
811	<
812	<	force[0] = 0;
813	<	force[1] = 0;
814	<	force[2] = 0;
815	<
816	<	//modify the forces of unconstrained molecules
817	<	for (int i = 0; i < (int) (unconsMols.size()); i++){
818	<	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
819	<
820	<	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
821	<	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
822	<	force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],
823	<	totalFZ);
824	<	unconsAtoms[j]->addFrc(force);
825	<	}
826	<	}
827	<
828	<	//modify the forces of moving z-constrained molecules
829	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
830	<	if (states[i] == zcsMoving){
831	<	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
832	<
833	<	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
834	<	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
835	<	force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],
836	<	totalFZ);
837	<	movingZAtoms[j]->addFrc(force);
838	<	}
839	<	}
840	<	}
841	<	}
842	<
843	<
844	<	template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
845	<	double force[3];
846	<	double harmonicU;
847	<	double harmonicF;
848	<	double COM[3];
849	<	double diff;
850	<	double totalFZ_local;
851	<	double totalFZ;
852	<
853	<	force[0] = 0;
854	<	force[1] = 0;
855	<	force[2] = 0;
856	<
857	<	totalFZ_local = 0;
858	<
859	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
860	<	if (states[i] == zcsMoving){
861	<	zconsMols[i]->getCOM(COM);
862	<
863	<	diff = COM[whichDirection] - resPos[i];
864	<
865	<	harmonicU = 0.5 * kz[i] * diff * diff;
866	<	info->lrPot += harmonicU;
867	<
868	<	harmonicF = -kz[i] * diff;
869	<	totalFZ_local += harmonicF;
870	<
871	<	//adjust force
872	<
873	<	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
874	<
875	<	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
876	<	force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
877	<	movingZAtoms[j],
878	<	harmonicF);
879	<	movingZAtoms[j]->addFrc(force);
880	<	}
881	<	}
882	<	}
883	<
884	<	#ifndef IS_MPI
885	<	totalFZ = totalFZ_local;
886	<	#else
887	<	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
888	<	#endif
889	<
890	<	force[0] = 0;
891	<	force[1] = 0;
892	<	force[2] = 0;
893	<
894	<	//modify the forces of unconstrained molecules
895	<	for (int i = 0; i < (int) (unconsMols.size()); i++){
896	<	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
897	<
898	<	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
899	<	//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
900	<	force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],
901	<	totalFZ);
902	<	unconsAtoms[j]->addFrc(force);
903	<	}
904	<	}
905	<
906	<	}
907	<
908	<	template<typename T> bool ZConstraint<T>::checkZConsState(){
909	<	double COM[3];
910	<	double diff;
911	<
912	<	int changed_local;
913	<	int changed;
914	<
915	<	changed_local = 0;
916	<
917	<	for (int i = 0; i < (int) (zconsMols.size()); i++){
918	<	zconsMols[i]->getCOM(COM);
919	<	diff = fabs(COM[whichDirection] - zPos[i]);
920	<	if (diff <= zconsTol && states[i] == zcsMoving){
921	<	states[i] = zcsFixed;
922	<	changed_local = 1;
923	<
924	<	if(usingSMD)
925	<	prevCantPos = cantPos;
926	<
927	<	if (hasZConsGap)
928	<	endFixTime[i] = info->getTime() + zconsFixTime;
929	<	}
930	<	else if (diff > zconsTol && states[i] == zcsFixed){
931	<	states[i] = zcsMoving;
932	<	changed_local = 1;
933	<
934	<	if(usingSMD)
935	<	cantPos = prevCantPos;
936	<
937	<	if (hasZConsGap)
938	<	endFixTime[i] = INFINITE_TIME;
939	<	}
940	<	}
941	<
942	<	#ifndef IS_MPI
943	<	changed = changed_local;
944	<	#else
945	<	MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
946	<	#endif
947	<
948	<	return (changed > 0);
949	<	}
950	<
951	<	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
952	<	int havingFixed_local;
953	<	int havingFixed;
954	<
955	<	havingFixed_local = 0;
956	<
957	<	for (int i = 0; i < (int) (zconsMols.size()); i++)
958	<	if (states[i] == zcsFixed){
959	<	havingFixed_local = 1;
960	<	break;
961	<	}
962	<
963	<	#ifndef IS_MPI
964	<	havingFixed = havingFixed_local;
965	<	#else
966	<	MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
967	<	MPI_COMM_WORLD);
968	<	#endif
969	<
970	<	return (havingFixed > 0);
971	<	}
972	<
973	<
974	<	template<typename T> bool ZConstraint<T>::haveMovingZMols(){
975	<	int havingMoving_local;
976	<	int havingMoving;
977	<
978	<	havingMoving_local = 0;
979	<
980	<	for (int i = 0; i < (int) (zconsMols.size()); i++)
981	<	if (states[i] == zcsMoving){
982	<	havingMoving_local = 1;
983	<	break;
984	<	}
985	<
986	<	#ifndef IS_MPI
987	<	havingMoving = havingMoving_local;
988	<	#else
989	<	MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
990	<	MPI_COMM_WORLD);
991	<	#endif
992	<
993	<	return (havingMoving > 0);
994	<	}
995	<
996	<
997	<	template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
998	<	double MVzOfMovingMols_local;
999	<	double MVzOfMovingMols;
1000	<	double totalMassOfMovingZMols_local;
1001	<	double totalMassOfMovingZMols;
1002	<	double COMvel[3];
1003	<
1004	<	MVzOfMovingMols_local = 0;
1005	<	totalMassOfMovingZMols_local = 0;
1006	<
1007	<	for (int i = 0; i < unconsMols.size(); i++){
1008	<	unconsMols[i]->getCOMvel(COMvel);
1009	<	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
1010	<	}
1011	<
1012	<	for (int i = 0; i < zconsMols.size(); i++){
1013	<	if (states[i] == zcsMoving){
1014	<	zconsMols[i]->getCOMvel(COMvel);
1015	<	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
1016	<	totalMassOfMovingZMols_local += massOfZConsMols[i];
1017	<	}
1018	<	}
1019	<
1020	<	#ifndef IS_MPI
1021	<	MVzOfMovingMols = MVzOfMovingMols_local;
1022	<	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1023	<	#else
1024	<	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
1025	<	MPI_SUM, MPI_COMM_WORLD);
1026	<	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
1027	<	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1028	<	#endif
1029	<
1030	<	double vzOfMovingMols;
1031	<	vzOfMovingMols = MVzOfMovingMols /
1032	<	(totalMassOfUncons + totalMassOfMovingZMols);
1033	<
1034	<	return vzOfMovingMols;
1035	<	}
1036	<
1037	<	template<typename T> double ZConstraint<T>::calcSysCOMVel(){
1038	<	double COMvel[3];
1039	<	double tempMVz_local;
1040	<	double tempMVz;
1041	<	double massOfZCons_local;
1042	<	double massOfZCons;
1043	<
1044	<
1045	<	tempMVz_local = 0;
1046	<
1047	<	for (int i = 0 ; i < nMols; i++){
1048	<	molecules[i].getCOMvel(COMvel);
1049	<	tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];
1050	<	}
1051	<
1052	<	massOfZCons_local = 0;
1053	<
1054	<	for (int i = 0; i < (int) (massOfZConsMols.size()); i++){
1055	<	massOfZCons_local += massOfZConsMols[i];
1056	<	}
1057	<	#ifndef IS_MPI
1058	<	massOfZCons = massOfZCons_local;
1059	<	tempMVz = tempMVz_local;
1060	<	#else
1061	<	MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,
1062	<	MPI_COMM_WORLD);
1063	<	MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1064	<	#endif
1065	<
1066	<	return tempMVz / (totalMassOfUncons + massOfZCons);
1067	<	}
1068	<
1069	<	template<typename T> double ZConstraint<T>::calcTotalForce(){
1070	<	double force[3];
1071	<	double totalForce_local;
1072	<	double totalForce;
1073	<
1074	<	totalForce_local = 0;
1075	<
1076	<	for (int i = 0; i < nAtoms; i++){
1077	<	atoms[i]->getFrc(force);
1078	<	totalForce_local += force[whichDirection];
1079	<	}
1080	<
1081	<	#ifndef IS_MPI
1082	<	totalForce = totalForce_local;
1083	<	#else
1084	<	MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,
1085	<	MPI_COMM_WORLD);
1086	<	#endif
1087	<
1088	<	return totalForce;
1089	<	}
1090	<
1091	<	template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1092	<	//calculate the number of atoms of moving z-constrained molecules
1093	<	int nMovingZAtoms_local;
1094	<	int nMovingZAtoms;
1095	<
1096	<	nMovingZAtoms_local = 0;
1097	<	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1098	<	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1099	<	nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1100	<	}
1101	<
1102	<	#ifdef IS_MPI
1103	<	MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,
1104	<	MPI_COMM_WORLD);
1105	<	#else
1106	<	nMovingZAtoms = nMovingZAtoms_local;
1107	<	#endif
1108	<	totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1109	<	}
1110	<
1111	<	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,
1112	<	Atom* atom,
1113	<	double totalForce){
1114	<	return totalForce / mol->getNAtoms();
1115	<	}
1116	<
1117	<	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,
1118	<	double totalForce){
1119	<	return totalForce / totNumOfMovingAtoms;
1120	<	}
1121	<
1122	<	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,
1123	<	Atom* atom,
1124	<	double totalForce){
1125	<	return totalForce / mol->getNAtoms();
1126	<	}
1127	<
1128	<	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,
1129	<	double totalForce){
1130	<	return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1131	<	}
1132	<
1133	<
1134	<	template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1135	<	//calculate the number of atoms of moving z-constrained molecules
1136	<	double massOfMovingZAtoms_local;
1137	<	double massOfMovingZAtoms;
1138	<
1139	<	massOfMovingZAtoms_local = 0;
1140	<	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1141	<	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1142	<	massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1143	<	}
1144	<
1145	<	#ifdef IS_MPI
1146	<	MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,
1147	<	MPI_SUM, MPI_COMM_WORLD);
1148	<	#else
1149	<	massOfMovingZAtoms = massOfMovingZAtoms_local;
1150	<	#endif
1151	<	totMassOfMovingAtoms = massOfMovingZAtoms +
1152	<	zconsIntegrator->totalMassOfUncons;
1153	<	}
1154	<
1155	<	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,
1156	<	Atom* atom,
1157	<	double totalForce){
1158	<	return totalForce * atom->getMass() / mol->getTotalMass();
1159	<	}
1160	<
1161	<	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,
1162	<	double totalForce){
1163	<	return totalForce * atom->getMass() / totMassOfMovingAtoms;
1164	<	}
1165	<
1166	<	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,
1167	<	Atom* atom,
1168	<	double totalForce){
1169	<	return totalForce * atom->getMass() / mol->getTotalMass();
1170	<	}
1171	<
1172	<	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,
1173	<	double totalForce){
1174	<	return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1175	<	}
1176	<
1177	<	template<typename T> void ZConstraint<T>::updateZPos(){
1178	<	double curTime;
1179	<	double COM[3];
1180	<
1181	<	curTime = info->getTime();
1182	<
1183	<	for (size_t i = 0; i < zconsMols.size(); i++){
1184	<
1185	<	if (states[i] == zcsFixed && curTime >= endFixTime[i]){
1186	<	zPos[i] += zconsGap;
1187	<
1188	<	if (usingSMD){
1189	<	zconsMols[i]->getCOM(COM);
1190	<	cantPos[i] = COM[whichDirection];
1191	<	}
1192	<
1193	<	}
1194	<
1195	<	}
1196	<
1197	<	}
1198	<
1199	<	template<typename T> void ZConstraint<T>::updateCantPos(){
1200	<	double curTime;
1201	<	double dt;
1202	<
1203	<	curTime = info->getTime();
1204	<	dt = info->dt;
1205	<
1206	<	for (size_t i = 0; i < zconsMols.size(); i++){
1207	<	if (states[i] == zcsMoving){
1208	<	cantPos[i] += cantVel[i] * dt;
1209	<	}
1210	<	}
1211	<
1212	<	}
1	>	#include "integrators/Integrator.hpp"
2	>	#include "utils/simError.h"
3	>	#include <math.h>
4	>
5	>	const double INFINITE_TIME = 10e30;
6	>	template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo,
7	>	ForceFields* the_ff): T(theInfo, the_ff),
8	>	fzOut(NULL),
9	>	curZconsTime(0),
10	>	forcePolicy(NULL),
11	>	usingSMD(false),
12	>	hasZConsGap(false){
13	>	//get properties from SimInfo
14	>	GenericData* data;
15	>	ZConsParaData* zConsParaData;
16	>	DoubleGenericData* sampleTime;
17	>	DoubleGenericData* tolerance;
18	>	DoubleGenericData* gap;
19	>	DoubleGenericData* fixtime;
20	>	StringGenericData* policy;
21	>	StringGenericData* filename;
22	>	IntGenericData* smdFlag;
23	>	double COM[3];
24	>
25	>	//by default, the direction of constraint is z
26	>	// 0 --> x
27	>	// 1 --> y
28	>	// 2 --> z
29	>	whichDirection = 2;
30	>
31	>	//estimate the force constant of harmonical potential
32	>	double Kb = 1.986E-3 ; //in kcal/K
33	>
34	>	double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /
35	>	2;
36	>	zForceConst = Kb * info->target_temp / (halfOfLargestBox * halfOfLargestBox);
37	>
38	>	//creat force Subtraction policy
39	>	data = info->getProperty(ZCONSFORCEPOLICY_ID);
40	>	if (!data){
41	>	sprintf(painCave.errMsg,
42	>	"ZConstraint Warning: User does not set force Subtraction policy, "
43	>	"PolicyByMass is used\n");
44	>	painCave.isFatal = 0;
45	>	simError();
46	>
47	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
48	>	}
49	>	else{
50	>	policy = dynamic_cast<StringGenericData*>(data);
51	>
52	>	if (!policy){
53	>	sprintf(painCave.errMsg,
54	>	"ZConstraint Error: Convertion from GenericData to StringGenericData failure, "
55	>	"PolicyByMass is used\n");
56	>	painCave.isFatal = 0;
57	>	simError();
58	>
59	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
60	>	}
61	>	else{
62	>	if (policy->getData() == "BYNUMBER")
63	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByNumber(this);
64	>	else if (policy->getData() == "BYMASS")
65	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
66	>	else{
67	>	sprintf(painCave.errMsg,
68	>	"ZConstraint Warning: unknown force Subtraction policy, "
69	>	"PolicyByMass is used\n");
70	>	painCave.isFatal = 0;
71	>	simError();
72	>	forcePolicy = (ForceSubtractionPolicy *) new PolicyByMass(this);
73	>	}
74	>	}
75	>	}
76	>
77	>
78	>	//retrieve sample time of z-contraint
79	>	data = info->getProperty(ZCONSTIME_ID);
80	>
81	>	if (!data){
82	>	sprintf(painCave.errMsg,
83	>	"ZConstraint error: If you use an ZConstraint\n"
84	>	" , you must set sample time.\n");
85	>	painCave.isFatal = 1;
86	>	simError();
87	>	}
88	>	else{
89	>	sampleTime = dynamic_cast<DoubleGenericData*>(data);
90	>
91	>	if (!sampleTime){
92	>	sprintf(painCave.errMsg,
93	>	"ZConstraint error: Can not get property from SimInfo\n");
94	>	painCave.isFatal = 1;
95	>	simError();
96	>	}
97	>	else{
98	>	this->zconsTime = sampleTime->getData();
99	>	}
100	>	}
101	>
102	>	//retrieve output filename of z force
103	>	data = info->getProperty(ZCONSFILENAME_ID);
104	>	if (!data){
105	>	sprintf(painCave.errMsg,
106	>	"ZConstraint error: If you use an ZConstraint\n"
107	>	" , you must set output filename of z-force.\n");
108	>	painCave.isFatal = 1;
109	>	simError();
110	>	}
111	>	else{
112	>	filename = dynamic_cast<StringGenericData*>(data);
113	>
114	>	if (!filename){
115	>	sprintf(painCave.errMsg,
116	>	"ZConstraint error: Can not get property from SimInfo\n");
117	>	painCave.isFatal = 1;
118	>	simError();
119	>	}
120	>	else{
121	>	this->zconsOutput = filename->getData();
122	>	}
123	>	}
124	>
125	>	//retrieve tolerance for z-constraint molecuels
126	>	data = info->getProperty(ZCONSTOL_ID);
127	>
128	>	if (!data){
129	>	sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n");
130	>	painCave.isFatal = 1;
131	>	simError();
132	>	}
133	>	else{
134	>	tolerance = dynamic_cast<DoubleGenericData*>(data);
135	>
136	>	if (!tolerance){
137	>	sprintf(painCave.errMsg,
138	>	"ZConstraint error: Can not get property from SimInfo\n");
139	>	painCave.isFatal = 1;
140	>	simError();
141	>	}
142	>	else{
143	>	this->zconsTol = tolerance->getData();
144	>	}
145	>	}
146	>
147	>	//quick hack here
148	>	data = info->getProperty(ZCONSGAP_ID);
149	>
150	>	if (data){
151	>	gap = dynamic_cast<DoubleGenericData*>(data);
152	>
153	>	if (!gap){
154	>	sprintf(painCave.errMsg,
155	>	"ZConstraint error: Can not get property from SimInfo\n");
156	>	painCave.isFatal = 1;
157	>	simError();
158	>	}
159	>	else{
160	>	this->hasZConsGap = true;
161	>	this->zconsGap = gap->getData();
162	>	}
163	>	}
164	>
165	>
166	>
167	>	data = info->getProperty(ZCONSFIXTIME_ID);
168	>
169	>	if (data){
170	>	fixtime = dynamic_cast<DoubleGenericData*>(data);
171	>	if (!fixtime){
172	>	sprintf(painCave.errMsg,
173	>	"ZConstraint error: Can not get zconsFixTime from SimInfo\n");
174	>	painCave.isFatal = 1;
175	>	simError();
176	>	}
177	>	else{
178	>	this->zconsFixTime = fixtime->getData();
179	>	}
180	>	}
181	>	else if(hasZConsGap){
182	>	sprintf(painCave.errMsg,
183	>	"ZConstraint error: must set fixtime if already set zconsGap\n");
184	>	painCave.isFatal = 1;
185	>	simError();
186	>	}
187	>
188	>
189	>
190	>	data = info->getProperty(ZCONSUSINGSMD_ID);
191	>
192	>	if (data){
193	>	smdFlag = dynamic_cast<IntGenericData*>(data);
194	>
195	>	if (!smdFlag){
196	>	sprintf(painCave.errMsg,
197	>	"ZConstraint error: Can not get property from SimInfo\n");
198	>	painCave.isFatal = 1;
199	>	simError();
200	>	}
201	>	else{
202	>	this->usingSMD= smdFlag->getData() ? true : false;
203	>	}
204	>
205	>	}
206	>
207	>
208	>
209	>	//retrieve index of z-constraint molecules
210	>	data = info->getProperty(ZCONSPARADATA_ID);
211	>	if (!data){
212	>	sprintf(painCave.errMsg,
213	>	"ZConstraint error: If you use an ZConstraint\n"
214	>	" , you must set index of z-constraint molecules.\n");
215	>	painCave.isFatal = 1;
216	>	simError();
217	>	}
218	>	else{
219	>	zConsParaData = dynamic_cast<ZConsParaData*>(data);
220	>
221	>	if (!zConsParaData){
222	>	sprintf(painCave.errMsg,
223	>	"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	else{
228	>	parameters = zConsParaData->getData();
229	>
230	>	//check the range of zconsIndex
231	>	//and the minimum value of index is the first one (we already sorted the data)
232	>	//the maximum value of index is the last one
233	>
234	>	int maxIndex;
235	>	int minIndex;
236	>	int totalNumMol;
237	>
238	>	minIndex = (*parameters)[0].zconsIndex;
239	>	if (minIndex < 0){
240	>	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
241	>	painCave.isFatal = 1;
242	>	simError();
243	>	}
244	>
245	>	maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
246	>
247	>	#ifndef IS_MPI
248	>	totalNumMol = nMols;
249	>	#else
250	>	totalNumMol = mpiSim->getNMolGlobal();
251	>	#endif
252	>
253	>	if (maxIndex > totalNumMol - 1){
254	>	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
255	>	painCave.isFatal = 1;
256	>	simError();
257	>	}
258	>
259	>	//if user does not specify the zpos for the zconstraint molecule
260	>	//its initial z coordinate  will be used as default
261	>	for (int i = 0; i < (int) (parameters->size()); i++){
262	>	if (!(*parameters)[i].havingZPos){
263	>	#ifndef IS_MPI
264	>	for (int j = 0; j < nMols; j++){
265	>	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
266	>	molecules[j].getCOM(COM);
267	>	break;
268	>	}
269	>	}
270	>	#else
271	>	//query which processor current zconstraint molecule belongs to
272	>	int* MolToProcMap;
273	>	int whichNode;
274	>
275	>	MolToProcMap = mpiSim->getMolToProcMap();
276	>	whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
277	>
278	>	//broadcast the zpos of current z-contraint molecule
279	>	//the node which contain this
280	>
281	>	if (worldRank == whichNode){
282	>	for (int j = 0; j < nMols; j++)
283	>	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
284	>	molecules[j].getCOM(COM);
285	>	break;
286	>	}
287	>	}
288	>
289	>	MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode,
290	>	MPI_COMM_WORLD);
291	>	#endif
292	>
293	>	(*parameters)[i].zPos = COM[whichDirection];
294	>
295	>	sprintf(painCave.errMsg,
296	>	"ZConstraint warning: Does not specify zpos for z-constraint molecule "
297	>	"initial z coornidate will be used \n");
298	>	painCave.isFatal = 0;
299	>	simError();
300	>	}
301	>	}
302	>	}//end if (!zConsParaData)
303	>
304	>	}//end  if (!data)
305	>
306	>	//
307	>	#ifdef IS_MPI
308	>	update();
309	>	#else
310	>	int searchResult;
311	>
312	>	for (int i = 0; i < nMols; i++){
313	>	searchResult = isZConstraintMol(&molecules[i]);
314	>
315	>	if (searchResult > -1){
316	>	zconsMols.push_back(&molecules[i]);
317	>	massOfZConsMols.push_back(molecules[i].getTotalMass());
318	>
319	>	zPos.push_back((*parameters)[searchResult].zPos);
320	>	kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
321	>
322	>	if(usingSMD)
323	>	cantVel.push_back((*parameters)[searchResult].cantVel);
324	>
325	>	}
326	>	else{
327	>	unconsMols.push_back(&molecules[i]);
328	>	massOfUnconsMols.push_back(molecules[i].getTotalMass());
329	>	}
330	>	}
331	>
332	>	fz.resize(zconsMols.size());
333	>	curZPos.resize(zconsMols.size());
334	>	indexOfZConsMols.resize(zconsMols.size());
335	>
336	>	//determine the states of z-constraint molecules
337	>	for (size_t i = 0; i < zconsMols.size(); i++){
338	>	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
339	>
340	>	zconsMols[i]->getCOM(COM);
341	>
342	>	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
343	>	states.push_back(zcsFixed);
344	>
345	>	if (hasZConsGap)
346	>	endFixTime.push_back(info->getTime() + zconsFixTime);
347	>	}
348	>	else{
349	>	states.push_back(zcsMoving);
350	>
351	>	if (hasZConsGap)
352	>	endFixTime.push_back(INFINITE_TIME);
353	>	}
354	>
355	>	if(usingSMD)
356	>	cantPos.push_back(COM[whichDirection]);
357	>	}
358	>
359	>	if(usingSMD)
360	>	prevCantPos = cantPos;
361	>	#endif
362	>
363	>
364	>	//get total masss of unconstraint molecules
365	>	double totalMassOfUncons_local;
366	>	totalMassOfUncons_local = 0;
367	>
368	>	for (size_t i = 0; i < unconsMols.size(); i++)
369	>	totalMassOfUncons_local += unconsMols[i]->getTotalMass();
370	>
371	>	#ifndef IS_MPI
372	>	totalMassOfUncons = totalMassOfUncons_local;
373	>	#else
374	>	MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,
375	>	MPI_SUM, MPI_COMM_WORLD);
376	>	#endif
377	>
378	>	//get total number of unconstrained atoms
379	>	int nUnconsAtoms_local;
380	>	nUnconsAtoms_local = 0;
381	>	for (int i = 0; i < (int) (unconsMols.size()); i++)
382	>	nUnconsAtoms_local += unconsMols[i]->getNAtoms();
383	>
384	>	#ifndef IS_MPI
385	>	totNumOfUnconsAtoms = nUnconsAtoms_local;
386	>	#else
387	>	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM,
388	>	MPI_COMM_WORLD);
389	>	#endif
390	>
391	>	forcePolicy->update();
392	>	}
393	>
394	>	template<typename T> ZConstraint<T>::~ZConstraint(){
395	>
396	>	if (fzOut){
397	>	delete fzOut;
398	>	}
399	>
400	>	if (forcePolicy){
401	>	delete forcePolicy;
402	>	}
403	>	}
404	>
405	>
406	>	/**
407	>	*
408	>	*/
409	>
410	>	#ifdef IS_MPI
411	>	template<typename T> void ZConstraint<T>::update(){
412	>	double COM[3];
413	>	int index;
414	>
415	>	zconsMols.clear();
416	>	massOfZConsMols.clear();
417	>	zPos.clear();
418	>	kz.clear();
419	>	cantPos.clear();
420	>	cantVel.clear();
421	>
422	>	unconsMols.clear();
423	>	massOfUnconsMols.clear();
424	>
425	>
426	>	//creat zconsMol and unconsMol lists
427	>	for (int i = 0; i < nMols; i++){
428	>	index = isZConstraintMol(&molecules[i]);
429	>
430	>	if (index > -1){
431	>	zconsMols.push_back(&molecules[i]);
432	>	zPos.push_back((*parameters)[index].zPos);
433	>	kz.push_back((*parameters)[index].kRatio * zForceConst);
434	>	massOfZConsMols.push_back(molecules[i].getTotalMass());
435	>
436	>	if(usingSMD)
437	>	cantVel.push_back((*parameters)[index].cantVel);
438	>
439	>	}
440	>	else{
441	>	unconsMols.push_back(&molecules[i]);
442	>	massOfUnconsMols.push_back(molecules[i].getTotalMass());
443	>	}
444	>	}
445	>
446	>	fz.resize(zconsMols.size());
447	>	curZPos.resize(zconsMols.size());
448	>	indexOfZConsMols.resize(zconsMols.size());
449	>
450	>	for (size_t i = 0; i < zconsMols.size(); i++){
451	>	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
452	>	}
453	>
454	>	//determine the states of z-constraint molecules
455	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
456	>
457	>	zconsMols[i]->getCOM(COM);
458	>
459	>	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol){
460	>	states.push_back(zcsFixed);
461	>
462	>	if (hasZConsGap)
463	>	endFixTime.push_back(info->getTime() + zconsFixTime);
464	>	}
465	>	else{
466	>	states.push_back(zcsMoving);
467	>
468	>	if (hasZConsGap)
469	>	endFixTime.push_back(INFINITE_TIME);
470	>	}
471	>
472	>	if(usingSMD)
473	>	cantPos.push_back(COM[whichDirection]);
474	>	}
475	>
476	>	if(usingSMD)
477	>	prevCantPos = cantPos;
478	>
479	>	forcePolicy->update();
480	>	}
481	>
482	>	#endif
483	>
484	>	/**
485	>	*  Function Name: isZConstraintMol
486	>	*  Parameter
487	>	*    Molecule* mol
488	>	*  Return value:
489	>	*    -1, if the molecule is not z-constraint molecule,
490	>	*    other non-negative values, its index in indexOfAllZConsMols vector
491	>	*/
492	>
493	>	template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){
494	>	int index;
495	>	int low;
496	>	int high;
497	>	int mid;
498	>
499	>	index = mol->getGlobalIndex();
500	>
501	>	low = 0;
502	>	high = parameters->size() - 1;
503	>
504	>	//Binary Search (we have sorted the array)
505	>	while (low <= high){
506	>	mid = (low + high) / 2;
507	>	if ((*parameters)[mid].zconsIndex == index)
508	>	return mid;
509	>	else if ((*parameters)[mid].zconsIndex > index)
510	>	high = mid - 1;
511	>	else
512	>	low = mid + 1;
513	>	}
514	>
515	>	return -1;
516	>	}
517	>
518	>	template<typename T> void ZConstraint<T>::integrate(){
519	>	// creat zconsWriter
520	>	fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
521	>
522	>	if (!fzOut){
523	>	sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");
524	>	painCave.isFatal = 1;
525	>	simError();
526	>	}
527	>
528	>	//zero out the velocities of center of mass of unconstrained molecules
529	>	//and the velocities of center of mass of every single z-constrained molecueles
530	>	zeroOutVel();
531	>
532	>	curZconsTime = zconsTime + info->getTime();
533	>
534	>	T::integrate();
535	>	}
536	>
537	>	template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
538	>	double zsys;
539	>	double COM[3];
540	>	double force[3];
541	>	double zSysCOMVel;
542	>
543	>	T::calcForce(calcPot, calcStress);
544	>
545	>
546	>	if (hasZConsGap){
547	>	updateZPos();
548	>	}
549	>
550	>	if (checkZConsState()){
551	>	zeroOutVel();
552	>	forcePolicy->update();
553	>	}
554	>
555	>	zsys = calcZSys();
556	>	zSysCOMVel = calcSysCOMVel();
557	>	#ifdef IS_MPI
558	>	if (worldRank == 0){
559	>	#endif
560	>
561	>	#ifdef IS_MPI
562	>	}
563	>	#endif
564	>
565	>	//do zconstraint force;
566	>	if (haveFixedZMols()){
567	>	this->doZconstraintForce();
568	>	}
569	>
570	>	//use external force to move the molecules to the specified positions
571	>	if (haveMovingZMols()){
572	>	if (usingSMD)
573	>	this->doHarmonic(cantPos);
574	>	else
575	>	this->doHarmonic(zPos);
576	>	}
577	>
578	>	//write out forces and current positions of z-constraint molecules
579	>	if (info->getTime() >= curZconsTime){
580	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
581	>	zconsMols[i]->getCOM(COM);
582	>	curZPos[i] = COM[whichDirection];
583	>
584	>	//if the z-constraint molecule is still moving, just record its force
585	>	if (states[i] == zcsMoving){
586	>	fz[i] = 0;
587	>	Atom** movingZAtoms;
588	>	movingZAtoms = zconsMols[i]->getMyAtoms();
589	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
590	>	movingZAtoms[j]->getFrc(force);
591	>	fz[i] += force[whichDirection];
592	>	}
593	>	}
594	>	}
595	>	fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],
596	>	&curZPos[0], &zPos[0]);
597	>	curZconsTime += zconsTime;
598	>	}
599	>
600	>	zSysCOMVel = calcSysCOMVel();
601	>	#ifdef IS_MPI
602	>	if (worldRank == 0){
603	>	#endif
604	>	#ifdef IS_MPI
605	>	}
606	>	#endif
607	>	}
608	>
609	>
610	>	template<typename T> double ZConstraint<T>::calcZSys(){
611	>	//calculate reference z coordinate for z-constraint molecules
612	>	double totalMass_local;
613	>	double totalMass;
614	>	double totalMZ_local;
615	>	double totalMZ;
616	>	double massOfCurMol;
617	>	double COM[3];
618	>
619	>	totalMass_local = 0;
620	>	totalMZ_local = 0;
621	>
622	>	for (int i = 0; i < nMols; i++){
623	>	massOfCurMol = molecules[i].getTotalMass();
624	>	molecules[i].getCOM(COM);
625	>
626	>	totalMass_local += massOfCurMol;
627	>	totalMZ_local += massOfCurMol * COM[whichDirection];
628	>	}
629	>
630	>
631	>	#ifdef IS_MPI
632	>	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,
633	>	MPI_COMM_WORLD);
634	>	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
635	>	#else
636	>	totalMass = totalMass_local;
637	>	totalMZ = totalMZ_local;
638	>	#endif
639	>
640	>	double zsys;
641	>	zsys = totalMZ / totalMass;
642	>
643	>	return zsys;
644	>	}
645	>
646	>	template<typename T> void ZConstraint<T>::thermalize(void){
647	>	T::thermalize();
648	>	zeroOutVel();
649	>	}
650	>
651	>	template<typename T> void ZConstraint<T>::zeroOutVel(){
652	>	Atom** fixedZAtoms;
653	>	double COMvel[3];
654	>	double vel[3];
655	>	double zSysCOMVel;
656	>
657	>	//zero out the velocities of center of mass of fixed z-constrained molecules
658	>
659	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
660	>	if (states[i] == zcsFixed){
661	>	zconsMols[i]->getCOMvel(COMvel);
662	>	//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
663	>
664	>	fixedZAtoms = zconsMols[i]->getMyAtoms();
665	>
666	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
667	>	vel = fixedZAtoms[j]->getVel();
668	>	vel[whichDirection] -= COMvel[whichDirection];
669	>	fixedZAtoms[j]->setVel(vel);
670	>	}
671	>
672	>	zconsMols[i]->getCOMvel(COMvel);
673	>	}
674	>	}
675	>
676	>	zSysCOMVel = calcSysCOMVel();
677	>	#ifdef IS_MPI
678	>	if (worldRank == 0){
679	>	#endif
680	>	#ifdef IS_MPI
681	>	}
682	>	#endif
683	>
684	>	// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
685	>	double MVzOfMovingMols_local;
686	>	double MVzOfMovingMols;
687	>	double totalMassOfMovingZMols_local;
688	>	double totalMassOfMovingZMols;
689	>
690	>	MVzOfMovingMols_local = 0;
691	>	totalMassOfMovingZMols_local = 0;
692	>
693	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
694	>	unconsMols[i]->getCOMvel(COMvel);
695	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
696	>	}
697	>
698	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
699	>	if (states[i] == zcsMoving){
700	>	zconsMols[i]->getCOMvel(COMvel);
701	>	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
702	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
703	>	}
704	>	}
705	>
706	>	#ifndef IS_MPI
707	>	MVzOfMovingMols = MVzOfMovingMols_local;
708	>	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
709	>	#else
710	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
711	>	MPI_SUM, MPI_COMM_WORLD);
712	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
713	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
714	>	#endif
715	>
716	>	double vzOfMovingMols;
717	>	vzOfMovingMols = MVzOfMovingMols /
718	>	(totalMassOfUncons + totalMassOfMovingZMols);
719	>
720	>	//modify the velocites of unconstrained molecules
721	>	Atom** unconsAtoms;
722	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
723	>	unconsAtoms = unconsMols[i]->getMyAtoms();
724	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
725	>	vel = unconsAtoms[j]->getVel();
726	>	vel[whichDirection] -= vzOfMovingMols;
727	>	unconsAtoms[j]->setVel(vel);
728	>	}
729	>	}
730	>
731	>	//modify the velocities of moving z-constrained molecuels
732	>	Atom** movingZAtoms;
733	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
734	>	if (states[i] == zcsMoving){
735	>	movingZAtoms = zconsMols[i]->getMyAtoms();
736	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
737	>	vel = movingZAtoms[j]->getVel();
738	>	vel[whichDirection] -= vzOfMovingMols;
739	>	movingZAtoms[j]->setVel(vel);
740	>	}
741	>	}
742	>	}
743	>
744	>
745	>	zSysCOMVel = calcSysCOMVel();
746	>	#ifdef IS_MPI
747	>	if (worldRank == 0){
748	>	#endif
749	>	#ifdef IS_MPI
750	>	}
751	>	#endif
752	>	}
753	>
754	>
755	>	template<typename T> void ZConstraint<T>::doZconstraintForce(){
756	>	Atom** zconsAtoms;
757	>	double totalFZ;
758	>	double totalFZ_local;
759	>	double COM[3];
760	>	double force[3];
761	>
762	>	//constrain the molecules which do not reach the specified positions
763	>
764	>	//Zero Out the force of z-contrained molecules
765	>	totalFZ_local = 0;
766	>
767	>	//calculate the total z-contrained force of fixed z-contrained molecules
768	>
769	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
770	>	if (states[i] == zcsFixed){
771	>	zconsMols[i]->getCOM(COM);
772	>	zconsAtoms = zconsMols[i]->getMyAtoms();
773	>
774	>	fz[i] = 0;
775	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
776	>	zconsAtoms[j]->getFrc(force);
777	>	fz[i] += force[whichDirection];
778	>	}
779	>	totalFZ_local += fz[i];
780	>
781	>	}
782	>	}
783	>
784	>	//calculate total z-constraint force
785	>	#ifdef IS_MPI
786	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
787	>	#else
788	>	totalFZ = totalFZ_local;
789	>	#endif
790	>
791	>
792	>	// apply negative to fixed z-constrained molecues;
793	>	force[0] = 0;
794	>	force[1] = 0;
795	>	force[2] = 0;
796	>
797	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
798	>	if (states[i] == zcsFixed){
799	>	int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
800	>	zconsAtoms = zconsMols[i]->getMyAtoms();
801	>
802	>	for (int j = 0; j < nAtomOfCurZConsMol; j++){
803	>	//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
804	>	force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],
805	>	zconsAtoms[j],
806	>	fz[i]);
807	>	zconsAtoms[j]->addFrc(force);
808	>	}
809	>	}
810	>	}
811	>
812	>	force[0] = 0;
813	>	force[1] = 0;
814	>	force[2] = 0;
815	>
816	>	//modify the forces of unconstrained molecules
817	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
818	>	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
819	>
820	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
821	>	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
822	>	force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],
823	>	totalFZ);
824	>	unconsAtoms[j]->addFrc(force);
825	>	}
826	>	}
827	>
828	>	//modify the forces of moving z-constrained molecules
829	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
830	>	if (states[i] == zcsMoving){
831	>	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
832	>
833	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
834	>	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
835	>	force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],
836	>	totalFZ);
837	>	movingZAtoms[j]->addFrc(force);
838	>	}
839	>	}
840	>	}
841	>	}
842	>
843	>
844	>	template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
845	>	double force[3];
846	>	double harmonicU;
847	>	double harmonicF;
848	>	double COM[3];
849	>	double diff;
850	>	double totalFZ_local;
851	>	double totalFZ;
852	>
853	>	force[0] = 0;
854	>	force[1] = 0;
855	>	force[2] = 0;
856	>
857	>	totalFZ_local = 0;
858	>
859	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
860	>	if (states[i] == zcsMoving){
861	>	zconsMols[i]->getCOM(COM);
862	>
863	>	diff = COM[whichDirection] - resPos[i];
864	>
865	>	harmonicU = 0.5 * kz[i] * diff * diff;
866	>	info->lrPot += harmonicU;
867	>
868	>	harmonicF = -kz[i] * diff;
869	>	totalFZ_local += harmonicF;
870	>
871	>	//adjust force
872	>
873	>	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
874	>
875	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
876	>	force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
877	>	movingZAtoms[j],
878	>	harmonicF);
879	>	movingZAtoms[j]->addFrc(force);
880	>	}
881	>	}
882	>	}
883	>
884	>	#ifndef IS_MPI
885	>	totalFZ = totalFZ_local;
886	>	#else
887	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
888	>	#endif
889	>
890	>	force[0] = 0;
891	>	force[1] = 0;
892	>	force[2] = 0;
893	>
894	>	//modify the forces of unconstrained molecules
895	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
896	>	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
897	>
898	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
899	>	//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
900	>	force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],
901	>	totalFZ);
902	>	unconsAtoms[j]->addFrc(force);
903	>	}
904	>	}
905	>
906	>	}
907	>
908	>	template<typename T> bool ZConstraint<T>::checkZConsState(){
909	>	double COM[3];
910	>	double diff;
911	>
912	>	int changed_local;
913	>	int changed;
914	>
915	>	changed_local = 0;
916	>
917	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
918	>	zconsMols[i]->getCOM(COM);
919	>	diff = fabs(COM[whichDirection] - zPos[i]);
920	>	if (diff <= zconsTol && states[i] == zcsMoving){
921	>	states[i] = zcsFixed;
922	>	changed_local = 1;
923	>
924	>	if(usingSMD)
925	>	prevCantPos = cantPos;
926	>
927	>	if (hasZConsGap)
928	>	endFixTime[i] = info->getTime() + zconsFixTime;
929	>	}
930	>	else if (diff > zconsTol && states[i] == zcsFixed){
931	>	states[i] = zcsMoving;
932	>	changed_local = 1;
933	>
934	>	if(usingSMD)
935	>	cantPos = prevCantPos;
936	>
937	>	if (hasZConsGap)
938	>	endFixTime[i] = INFINITE_TIME;
939	>	}
940	>	}
941	>
942	>	#ifndef IS_MPI
943	>	changed = changed_local;
944	>	#else
945	>	MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
946	>	#endif
947	>
948	>	return (changed > 0);
949	>	}
950	>
951	>	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
952	>	int havingFixed_local;
953	>	int havingFixed;
954	>
955	>	havingFixed_local = 0;
956	>
957	>	for (int i = 0; i < (int) (zconsMols.size()); i++)
958	>	if (states[i] == zcsFixed){
959	>	havingFixed_local = 1;
960	>	break;
961	>	}
962	>
963	>	#ifndef IS_MPI
964	>	havingFixed = havingFixed_local;
965	>	#else
966	>	MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
967	>	MPI_COMM_WORLD);
968	>	#endif
969	>
970	>	return (havingFixed > 0);
971	>	}
972	>
973	>
974	>	template<typename T> bool ZConstraint<T>::haveMovingZMols(){
975	>	int havingMoving_local;
976	>	int havingMoving;
977	>
978	>	havingMoving_local = 0;
979	>
980	>	for (int i = 0; i < (int) (zconsMols.size()); i++)
981	>	if (states[i] == zcsMoving){
982	>	havingMoving_local = 1;
983	>	break;
984	>	}
985	>
986	>	#ifndef IS_MPI
987	>	havingMoving = havingMoving_local;
988	>	#else
989	>	MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
990	>	MPI_COMM_WORLD);
991	>	#endif
992	>
993	>	return (havingMoving > 0);
994	>	}
995	>
996	>
997	>	template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
998	>	double MVzOfMovingMols_local;
999	>	double MVzOfMovingMols;
1000	>	double totalMassOfMovingZMols_local;
1001	>	double totalMassOfMovingZMols;
1002	>	double COMvel[3];
1003	>
1004	>	MVzOfMovingMols_local = 0;
1005	>	totalMassOfMovingZMols_local = 0;
1006	>
1007	>	for (int i = 0; i < unconsMols.size(); i++){
1008	>	unconsMols[i]->getCOMvel(COMvel);
1009	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
1010	>	}
1011	>
1012	>	for (int i = 0; i < zconsMols.size(); i++){
1013	>	if (states[i] == zcsMoving){
1014	>	zconsMols[i]->getCOMvel(COMvel);
1015	>	MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
1016	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
1017	>	}
1018	>	}
1019	>
1020	>	#ifndef IS_MPI
1021	>	MVzOfMovingMols = MVzOfMovingMols_local;
1022	>	totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1023	>	#else
1024	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
1025	>	MPI_SUM, MPI_COMM_WORLD);
1026	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
1027	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1028	>	#endif
1029	>
1030	>	double vzOfMovingMols;
1031	>	vzOfMovingMols = MVzOfMovingMols /
1032	>	(totalMassOfUncons + totalMassOfMovingZMols);
1033	>
1034	>	return vzOfMovingMols;
1035	>	}
1036	>
1037	>	template<typename T> double ZConstraint<T>::calcSysCOMVel(){
1038	>	double COMvel[3];
1039	>	double tempMVz_local;
1040	>	double tempMVz;
1041	>	double massOfZCons_local;
1042	>	double massOfZCons;
1043	>
1044	>
1045	>	tempMVz_local = 0;
1046	>
1047	>	for (int i = 0 ; i < nMols; i++){
1048	>	molecules[i].getCOMvel(COMvel);
1049	>	tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];
1050	>	}
1051	>
1052	>	massOfZCons_local = 0;
1053	>
1054	>	for (int i = 0; i < (int) (massOfZConsMols.size()); i++){
1055	>	massOfZCons_local += massOfZConsMols[i];
1056	>	}
1057	>	#ifndef IS_MPI
1058	>	massOfZCons = massOfZCons_local;
1059	>	tempMVz = tempMVz_local;
1060	>	#else
1061	>	MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,
1062	>	MPI_COMM_WORLD);
1063	>	MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1064	>	#endif
1065	>
1066	>	return tempMVz / (totalMassOfUncons + massOfZCons);
1067	>	}
1068	>
1069	>	template<typename T> double ZConstraint<T>::calcTotalForce(){
1070	>	double force[3];
1071	>	double totalForce_local;
1072	>	double totalForce;
1073	>
1074	>	totalForce_local = 0;
1075	>
1076	>	for (int i = 0; i < nAtoms; i++){
1077	>	atoms[i]->getFrc(force);
1078	>	totalForce_local += force[whichDirection];
1079	>	}
1080	>
1081	>	#ifndef IS_MPI
1082	>	totalForce = totalForce_local;
1083	>	#else
1084	>	MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,
1085	>	MPI_COMM_WORLD);
1086	>	#endif
1087	>
1088	>	return totalForce;
1089	>	}
1090	>
1091	>	template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1092	>	//calculate the number of atoms of moving z-constrained molecules
1093	>	int nMovingZAtoms_local;
1094	>	int nMovingZAtoms;
1095	>
1096	>	nMovingZAtoms_local = 0;
1097	>	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1098	>	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1099	>	nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1100	>	}
1101	>
1102	>	#ifdef IS_MPI
1103	>	MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,
1104	>	MPI_COMM_WORLD);
1105	>	#else
1106	>	nMovingZAtoms = nMovingZAtoms_local;
1107	>	#endif
1108	>	totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1109	>	}
1110	>
1111	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,
1112	>	Atom* atom,
1113	>	double totalForce){
1114	>	return totalForce / mol->getNAtoms();
1115	>	}
1116	>
1117	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,
1118	>	double totalForce){
1119	>	return totalForce / totNumOfMovingAtoms;
1120	>	}
1121	>
1122	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,
1123	>	Atom* atom,
1124	>	double totalForce){
1125	>	return totalForce / mol->getNAtoms();
1126	>	}
1127	>
1128	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,
1129	>	double totalForce){
1130	>	return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1131	>	}
1132	>
1133	>
1134	>	template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1135	>	//calculate the number of atoms of moving z-constrained molecules
1136	>	double massOfMovingZAtoms_local;
1137	>	double massOfMovingZAtoms;
1138	>
1139	>	massOfMovingZAtoms_local = 0;
1140	>	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1141	>	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1142	>	massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1143	>	}
1144	>
1145	>	#ifdef IS_MPI
1146	>	MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,
1147	>	MPI_SUM, MPI_COMM_WORLD);
1148	>	#else
1149	>	massOfMovingZAtoms = massOfMovingZAtoms_local;
1150	>	#endif
1151	>	totMassOfMovingAtoms = massOfMovingZAtoms +
1152	>	zconsIntegrator->totalMassOfUncons;
1153	>	}
1154	>
1155	>	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,
1156	>	Atom* atom,
1157	>	double totalForce){
1158	>	return totalForce * atom->getMass() / mol->getTotalMass();
1159	>	}
1160	>
1161	>	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,
1162	>	double totalForce){
1163	>	return totalForce * atom->getMass() / totMassOfMovingAtoms;
1164	>	}
1165	>
1166	>	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,
1167	>	Atom* atom,
1168	>	double totalForce){
1169	>	return totalForce * atom->getMass() / mol->getTotalMass();
1170	>	}
1171	>
1172	>	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,
1173	>	double totalForce){
1174	>	return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1175	>	}
1176	>
1177	>	template<typename T> void ZConstraint<T>::updateZPos(){
1178	>	double curTime;
1179	>	double COM[3];
1180	>
1181	>	curTime = info->getTime();
1182	>
1183	>	for (size_t i = 0; i < zconsMols.size(); i++){
1184	>
1185	>	if (states[i] == zcsFixed && curTime >= endFixTime[i]){
1186	>	zPos[i] += zconsGap;
1187	>
1188	>	if (usingSMD){
1189	>	zconsMols[i]->getCOM(COM);
1190	>	cantPos[i] = COM[whichDirection];
1191	>	}
1192	>
1193	>	}
1194	>
1195	>	}
1196	>
1197	>	}
1198	>
1199	>	template<typename T> void ZConstraint<T>::updateCantPos(){
1200	>	double curTime;
1201	>	double dt;
1202	>
1203	>	curTime = info->getTime();
1204	>	dt = info->dt;
1205	>
1206	>	for (size_t i = 0; i < zconsMols.size(); i++){
1207	>	if (states[i] == zcsMoving){
1208	>	cantPos[i] += cantVel[i] * dt;
1209	>	}
1210	>	}
1211	>
1212	>	}

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