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

Comparing trunk/OOPSE/libmdtools/ZConstraint.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 2004 UTC

#	Line 1 | Line 1
1		#include "Integrator.hpp"
2		#include "simError.h"
3	<	#include <cmath>
4	<	template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff)
5	<	: T(theInfo, the_ff), fz(NULL),
6	<	indexOfZConsMols(NULL)
7	<	{
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		DoubleData* sampleTime;
17		DoubleData* tolerance;
18	+	DoubleData* gap;
19	+	DoubleData* fixtime;
20	+	StringData* policy;
21		StringData* filename;
22	+	IntData* smdFlag;
23		double COM[3];
24
25		//by default, the direction of constraint is z
#	Line 22 | Line 30 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
30
31		//estimate the force constant of harmonical potential
32		double Kb = 1.986E-3 ; //in kcal/K
25	–
26	–	double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2;
27	–	zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox);
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<StringData*>(data);
51	+
52	+	if (!policy){
53	+	sprintf(painCave.errMsg,
54	+	"ZConstraint Error: Convertion from GenericData to StringData 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	<
83	<	sprintf( painCave.errMsg,
84	<	"ZConstraint error: If you use an ZConstraint\n"
36	<	" , you must set sample time.\n");
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();
86	>	simError();
87		}
88		else{
41	–
89		sampleTime = dynamic_cast<DoubleData*>(data);
43	–
44	–	if(!sampleTime){
90
91	<	sprintf( painCave.errMsg,
92	<	"ZConstraint error: Can not get property from SimInfo\n");
91	>	if (!sampleTime){
92	>	sprintf(painCave.errMsg,
93	>	"ZConstraint error: Can not get property from SimInfo\n");
94		painCave.isFatal = 1;
95	<	simError();
50	<
95	>	simError();
96		}
97		else{
98		this->zconsTime = sampleTime->getData();
99		}
55	–
100		}
101	<
101	>
102		//retrieve output filename of z force
103		data = info->getProperty(ZCONSFILENAME_ID);
104	<	if(!data) {
105	<
106	<
107	<	sprintf( painCave.errMsg,
64	<	"ZConstraint error: If you use an ZConstraint\n"
65	<	" , you must set output filename of z-force.\n");
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();
68	<
109	>	simError();
110		}
111		else{
112	+	filename = dynamic_cast<StringData*>(data);
113
114	<	filename = dynamic_cast<StringData*>(data);
115	<
116	<	if(!filename){
75	<
76	<	sprintf( painCave.errMsg,
77	<	"ZConstraint error: Can not get property from SimInfo\n");
114	>	if (!filename){
115	>	sprintf(painCave.errMsg,
116	>	"ZConstraint error: Can not get property from SimInfo\n");
117		painCave.isFatal = 1;
118	<	simError();
80	<
118	>	simError();
119		}
120		else{
121		this->zconsOutput = filename->getData();
122		}
85	–
86	–
123		}
124
125		//retrieve tolerance for z-constraint molecuels
126		data = info->getProperty(ZCONSTOL_ID);
127	<
128	<	if(!data) {
129	<
94	<	sprintf( painCave.errMsg,
95	<	"ZConstraint error: can not get tolerance \n");
127	>
128	>	if (!data){
129	>	sprintf(painCave.errMsg, "ZConstraint error: can not get tolerance \n");
130		painCave.isFatal = 1;
131	<	simError();
131	>	simError();
132		}
133		else{
100	–
134		tolerance = dynamic_cast<DoubleData*>(data);
102	–
103	–	if(!tolerance){
135
136	<	sprintf( painCave.errMsg,
137	<	"ZConstraint error: Can not get property from SimInfo\n");
136	>	if (!tolerance){
137	>	sprintf(painCave.errMsg,
138	>	"ZConstraint error: Can not get property from SimInfo\n");
139		painCave.isFatal = 1;
140	<	simError();
109	<
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<DoubleData*>(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	<
164	>
165	>
166	>
167	>	data = info->getProperty(ZCONSFIXTIME_ID);
168	>
169	>	if (data){
170	>	fixtime = dynamic_cast<DoubleData*>(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<IntData*>(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	<
213	<	sprintf( painCave.errMsg,
214	<	"ZConstraint error: If you use an ZConstraint\n"
123	<	" , you must set index of z-constraint molecules.\n");
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();
216	>	simError();
217		}
218		else{
128	–
219		zConsParaData = dynamic_cast<ZConsParaData*>(data);
130	–
131	–	if(!zConsParaData){
220
221	<	sprintf( painCave.errMsg,
222	<	"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n");
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();
137	<
225	>	simError();
226		}
227		else{
140	–
228		parameters = zConsParaData->getData();
229
230		//check the range of zconsIndex
#	Line 149 | Line 236 | template<typename T> ZConstraint<T>::ZConstraint(SimIn
236		int totalNumMol;
237
238		minIndex = (*parameters)[0].zconsIndex;
239	<	if(minIndex < 0){
240	<	sprintf( painCave.errMsg,
154	<	"ZConstraint error: index is out of range\n");
239	>	if (minIndex < 0){
240	>	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
241		painCave.isFatal = 1;
242	<	simError();
243	<	}
242	>	simError();
243	>	}
244
245		maxIndex = (*parameters)[parameters->size() - 1].zconsIndex;
246
247		#ifndef IS_MPI
248		totalNumMol = nMols;
249		#else
250	<	totalNumMol = mpiSim->getTotNmol();
250	>	totalNumMol = mpiSim->getNMolGlobal();
251		#endif
252	<
253	<	if(maxIndex > totalNumMol - 1){
254	<	sprintf( painCave.errMsg,
169	<	"ZConstraint error: index is out of range\n");
252	>
253	>	if (maxIndex > totalNumMol - 1){
254	>	sprintf(painCave.errMsg, "ZConstraint error: index is out of range\n");
255		painCave.isFatal = 1;
256	<	simError();
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 < parameters->size(); i++){
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	<	if(!(*parameters)[i].havingZPos){
275	>	MolToProcMap = mpiSim->getMolToProcMap();
276	>	whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
277
278	<	#ifndef IS_MPI
279	<	for(int j = 0; j < nMols; j++){
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;
284	>	molecules[j].getCOM(COM);
285	>	break;
286		}
287	<	}
187	<	#else
188	<	//query which processor current zconstraint molecule belongs to
189	<	int *MolToProcMap;
190	<	int whichNode;
191	<	double initZPos;
192	<	MolToProcMap = mpiSim->getMolToProcMap();
193	<	whichNode = MolToProcMap[(*parameters)[i].zconsIndex];
194	<
195	<	//broadcast the zpos of current z-contraint molecule
196	<	//the node which contain this
197	<
198	<	if (worldRank == whichNode ){
199	<
200	<	for(int j = 0; j < nMols; j++)
201	<	if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){
202	<	molecules[j].getCOM(COM);
203	<	break;
204	<	}
205	<
206	<	}
287	>	}
288
289	<	MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE_PRECISION, whichNode, MPI_COMM_WORLD);
289	>	MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode,
290	>	MPI_COMM_WORLD);
291		#endif
210	–
211	–	(*parameters)[i].zPos = COM[whichDirection];
292
293	<	sprintf( painCave.errMsg,
294	<	"ZConstraint warningr: Does not specify zpos for z-constraint molecule "
295	<	"initial z coornidate will be used \n");
296	<	painCave.isFatal = 0;
297	<	simError();
298	<
299	<	}
300	<	}
301	<
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	<	//
305	>
306	>	//
307		#ifdef IS_MPI
308		update();
309		#else
310		int searchResult;
311	<
312	<	for(int i = 0; i < nMols; i++){
232	<
311	>
312	>	for (int i = 0; i < nMols; i++){
313		searchResult = isZConstraintMol(&molecules[i]);
314	<
315	<	if(searchResult > -1){
236	<
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);
320	>	kz.push_back((*parameters)[searchResult]. kRatio * zForceConst);
321
322	<	molecules[i].getCOM(COM);
322	>	if(usingSMD)
323	>	cantVel.push_back((*parameters)[searchResult].cantVel);
324	>
325		}
326	<	else
246	<	{
247	<
326	>	else{
327		unconsMols.push_back(&molecules[i]);
328		massOfUnconsMols.push_back(molecules[i].getTotalMass());
250	–
329		}
330		}
331
332	<	fz = new double[zconsMols.size()];
333	<	indexOfZConsMols = new int [zconsMols.size()];
332	>	fz.resize(zconsMols.size());
333	>	curZPos.resize(zconsMols.size());
334	>	indexOfZConsMols.resize(zconsMols.size());
335
257	–	if(!fz || !indexOfZConsMols){
258	–	sprintf( painCave.errMsg,
259	–	"Memory allocation failure in class Zconstraint\n");
260	–	painCave.isFatal = 1;
261	–	simError();
262	–	}
263	–
336		//determine the states of z-constraint molecules
337	<	for(int i = 0; i < zconsMols.size(); i++){
337	>	for (size_t i = 0; i < zconsMols.size(); i++){
338		indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
339
340	<	zconsMols[i]->getCOM(COM);
341	<	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
342	<	states.push_back(zcsFixed);
343	<	else
344	<	states.push_back(zcsMoving);
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	<
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(int i = 0; i < unconsMols.size(); i++)
367	>
368	>	for (size_t i = 0; i < unconsMols.size(); i++)
369		totalMassOfUncons_local += unconsMols[i]->getTotalMass();
370	<
370	>
371		#ifndef IS_MPI
372		totalMassOfUncons = totalMassOfUncons_local;
373		#else
374	<	MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
374	>	MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,
375	>	MPI_SUM, MPI_COMM_WORLD);
376		#endif
377
290	–
378		//get total number of unconstrained atoms
379		int nUnconsAtoms_local;
380		nUnconsAtoms_local = 0;
381	<	for(int i = 0; i < unconsMols.size(); i++)
381	>	for (int i = 0; i < (int) (unconsMols.size()); i++)
382		nUnconsAtoms_local += unconsMols[i]->getNAtoms();
383	<
383	>
384		#ifndef IS_MPI
385		totNumOfUnconsAtoms = nUnconsAtoms_local;
386		#else
387	<	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
387	>	MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_INT, MPI_SUM,
388	>	MPI_COMM_WORLD);
389		#endif
390
391	<	// creat zconsWriter
304	<	fzOut = new ZConsWriter(zconsOutput.c_str());
305	<
306	<	if(!fzOut){
307	<	sprintf( painCave.errMsg,
308	<	"Memory allocation failure in class Zconstraint\n");
309	<	painCave.isFatal = 1;
310	<	simError();
311	<	}
312	<
391	>	forcePolicy->update();
392		}
393
394	<	template<typename T> ZConstraint<T>::~ZConstraint()
395	<	{
396	<	if(fz)
318	<	delete[] fz;
319	<
320	<	if(indexOfZConsMols)
321	<	delete[] indexOfZConsMols;
322	<
323	<	if(fzOut)
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()
329	<	{
411	>	template<typename T> void ZConstraint<T>::update(){
412		double COM[3];
413		int index;
414	<
414	>
415		zconsMols.clear();
416		massOfZConsMols.clear();
417		zPos.clear();
418		kz.clear();
419	<
419	>	cantPos.clear();
420	>	cantVel.clear();
421	>
422		unconsMols.clear();
423		massOfUnconsMols.clear();
340	–
424
425	+
426		//creat zconsMol and unconsMol lists
427	<	for(int i = 0; i < nMols; i++){
344	<
427	>	for (int i = 0; i < nMols; i++){
428		index = isZConstraintMol(&molecules[i]);
429	<
430	<	if(index > -1){
348	<
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	<
435	<	massOfZConsMols.push_back(molecules[i].getTotalMass());
436	<
437	<	molecules[i].getCOM(COM);
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
358	<	{
359	<
440	>	else{
441		unconsMols.push_back(&molecules[i]);
442		massOfUnconsMols.push_back(molecules[i].getTotalMass());
362	–
443		}
444		}
445
446	<	//determine the states of z-constraint molecules
447	<	for(int i = 0; i < zconsMols.size(); i++){
448	<	zconsMols[i]->getCOM(COM);
449	<	if (fabs(zPos[i] - COM[whichDirection]) < zconsTol)
450	<	states.push_back(zcsFixed);
451	<	else
372	<	states.push_back(zcsMoving);
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	<	//The reason to declare fz and indexOfZconsMols as pointer to array is
460	<	// that we want to make the MPI communication simple
461	<	if(fz)
462	<	delete[] fz;
463	<
381	<	if(indexOfZConsMols)
382	<	delete[] indexOfZConsMols;
383	<
384	<	if (zconsMols.size() > 0){
385	<	fz = new double[zconsMols.size()];
386	<	indexOfZConsMols =  new int[zconsMols.size()];
387	<
388	<	if(!fz || !indexOfZConsMols){
389	<	sprintf( painCave.errMsg,
390	<	"Memory allocation failure in class Zconstraint\n");
391	<	painCave.isFatal = 1;
392	<	simError();
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	<
466	<	for(int i = 0; i < zconsMols.size(); i++){
467	<	indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex();
465	>	else{
466	>	states.push_back(zcsMoving);
467	>
468	>	if (hasZConsGap)
469	>	endFixTime.push_back(INFINITE_TIME);
470		}
471
472	<	}
473	<	else{
474	<	fz = NULL;
475	<	indexOfZConsMols = NULL;
476	<	}
477	<
472	>	if(usingSMD)
473	>	cantPos.push_back(COM[whichDirection]);
474	>	}
475	>
476	>	if(usingSMD)
477	>	prevCantPos = cantPos;
478	>
479	>	//
480	>	forcePolicy->update();
481		}
482
483		#endif
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
485	>	/**
486	>	*  Function Name: isZConstraintMol
487	>	*  Parameter
488	>	*    Molecule* mol
489	>	*  Return value:
490	>	*    -1, if the molecule is not z-constraint molecule,
491	>	*    other non-negative values, its index in indexOfAllZConsMols vector
492		*/
493
494	<	template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol)
418	<	{
494	>	template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol){
495		int index;
496		int low;
497		int high;
498		int mid;
499
500		index = mol->getGlobalIndex();
501	<
501	>
502		low = 0;
503		high = parameters->size() - 1;
504	<
504	>
505		//Binary Search (we have sorted the array)
506	<	while(low <= high){
507	<	mid = (low + high) /2;
506	>	while (low <= high){
507	>	mid = (low + high) / 2;
508		if ((*parameters)[mid].zconsIndex == index)
509		return mid;
510	<	else if ((*parameters)[mid].zconsIndex > index )
511	<	high = mid -1;
512	<	else
513	<	low = mid + 1;
510	>	else if ((*parameters)[mid].zconsIndex > index)
511	>	high = mid - 1;
512	>	else
513	>	low = mid + 1;
514		}
515	<
515	>
516		return -1;
517		}
518
519		template<typename T> void ZConstraint<T>::integrate(){
520	<
520	>	// creat zconsWriter
521	>	fzOut = new ZConsWriter(zconsOutput.c_str(), parameters);
522	>
523	>	if (!fzOut){
524	>	sprintf(painCave.errMsg, "Memory allocation failure in class Zconstraint\n");
525	>	painCave.isFatal = 1;
526	>	simError();
527	>	}
528	>
529		//zero out the velocities of center of mass of unconstrained molecules
530		//and the velocities of center of mass of every single z-constrained molecueles
531		zeroOutVel();
448	–
449	–	T::integrate();
532
533	+	curZconsTime = zconsTime + info->getTime();
534	+
535	+	T::integrate();
536		}
452	–
537
538	+
539		/**
540		*
541		*
542		*
543		*
544	<	*/
460	<
461	<
544	>	*/
545		template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){
546		double zsys;
547	+	double COM[3];
548	+	double force[3];
549	+	double zSysCOMVel;
550
551		T::calcForce(calcPot, calcStress);
552
553	<	if (checkZConsState())
554	<	zeroOutVel();
555	<
553	>
554	>	if (hasZConsGap){
555	>	updateZPos();
556	>	}
557	>
558	>	if (checkZConsState()){
559	>	zeroOutVel();
560	>	forcePolicy->update();
561	>	}
562	>
563		zsys = calcZSys();
564	<	cout << "---------------------------------------------------------------------" <<endl;
565	<	cout << "current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl;
566	<	cout << "before calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
567	<
564	>	zSysCOMVel = calcSysCOMVel();
565	>	#ifdef IS_MPI
566	>	if (worldRank == 0){
567	>	#endif
568	>	//cout << "---------------------------------------------------------------------" <<endl;
569	>	//cout << "current time: " << info->getTime() << endl;
570	>	//cout << "center of mass at z: " << zsys << endl;
571	>	//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl;
572
573	+	#ifdef IS_MPI
574	+	}
575	+	#endif
576	+
577		//do zconstraint force;
578	<	if (haveFixedZMols())
578	>	if (haveFixedZMols()){
579		this->doZconstraintForce();
580	+	}
581
582	+	//use external force to move the molecules to the specified positions
583	+	if (haveMovingZMols()){
584	+	if (usingSMD)
585	+	this->doHarmonic(cantPos);
586	+	else
587	+	this->doHarmonic(zPos);
588	+	}
589
590	<
591	<	//use harmonical poteintial to move the molecules to the specified positions
592	<	if (haveMovingZMols())
593	<	this->doHarmonic();
594	<
595	<	fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz);
596	<	cout << "after calcForce, the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
590	>	//write out forces and current positions of z-constraint molecules
591	>	if (info->getTime() >= curZconsTime){
592	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
593	>	zconsMols[i]->getCOM(COM);
594	>	curZPos[i] = COM[whichDirection];
595	>
596	>	//if the z-constraint molecule is still moving, just record its force
597	>	if (states[i] == zcsMoving){
598	>	fz[i] = 0;
599	>	Atom** movingZAtoms;
600	>	movingZAtoms = zconsMols[i]->getMyAtoms();
601	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
602	>	movingZAtoms[j]->getFrc(force);
603	>	fz[i] += force[whichDirection];
604	>	}
605	>	}
606	>	}
607	>	fzOut->writeFZ(info->getTime(), zconsMols.size(), &indexOfZConsMols[0], &fz[0],
608	>	&curZPos[0], &zPos[0]);
609	>	curZconsTime += zconsTime;
610	>	}
611	>
612	>	zSysCOMVel = calcSysCOMVel();
613	>	#ifdef IS_MPI
614	>	if (worldRank == 0){
615	>	#endif
616	>	//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl;
617	>	#ifdef IS_MPI
618	>	}
619	>	#endif
620		}
621	<
622	<	template<typename T> double ZConstraint<T>::calcZSys()
623	<	{
621	>
622	>
623	>	/**
624	>	*
625	>	*/
626	>
627	>	template<typename T> double ZConstraint<T>::calcZSys(){
628		//calculate reference z coordinate for z-constraint molecules
629		double totalMass_local;
630		double totalMass;
631		double totalMZ_local;
632		double totalMZ;
497	–	double massOfUncons_local;
633		double massOfCurMol;
634		double COM[3];
635	<
635	>
636		totalMass_local = 0;
502	–	totalMass = 0;
637		totalMZ_local = 0;
638	<	totalMZ = 0;
639	<	massOfUncons_local = 0;
506	<
507	<
508	<	for(int i = 0; i < nMols; i++){
638	>
639	>	for (int i = 0; i < nMols; i++){
640		massOfCurMol = molecules[i].getTotalMass();
641		molecules[i].getCOM(COM);
642	<
642	>
643		totalMass_local += massOfCurMol;
644		totalMZ_local += massOfCurMol * COM[whichDirection];
514	–
515	–	if(isZConstraintMol(&molecules[i]) == -1){
516	–
517	–	massOfUncons_local += massOfCurMol;
518	–	}
519	–
645		}
646	<
647	<
646	>
647	>
648		#ifdef IS_MPI
649	<	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
650	<	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
651	<	MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
649	>	MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE, MPI_SUM,
650	>	MPI_COMM_WORLD);
651	>	MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
652		#else
653		totalMass = totalMass_local;
654		totalMZ = totalMZ_local;
530	–	totalMassOfUncons = massOfUncons_local;
655		#endif
656
657		double zsys;
#	Line 539 | Line 663 | template<typename T> double ZConstraint<T>::calcZSys()
663		/**
664		*
665		*/
666	<	template<typename T> void ZConstraint<T>::thermalize( void ){
543	<
666	>	template<typename T> void ZConstraint<T>::thermalize(void){
667		T::thermalize();
668		zeroOutVel();
669		}
670
671		/**
672		*
550	–	*
551	–	*
673		*/
674
675		template<typename T> void ZConstraint<T>::zeroOutVel(){
555	–
676		Atom** fixedZAtoms;
677		double COMvel[3];
678		double vel[3];
679	+	double zSysCOMVel;
680
560	–	double tempMass = 0;
561	–	double tempMVz =0;
562	–	double tempVz = 0;
563	–	for(int i = 0; i < nMols; i++){
564	–	molecules[i].getCOMvel(COMvel);
565	–	tempMass +=molecules[i].getTotalMass();
566	–	tempMVz += molecules[i].getTotalMass() * COMvel[whichDirection];
567	–	tempVz += COMvel[whichDirection];
568	–	}
569	–	cout << "initial velocity of center of mass is " << tempMVz / tempMass << endl;
570	–
681		//zero out the velocities of center of mass of fixed z-constrained molecules
572	–
573	–	for(int i = 0; i < zconsMols.size(); i++){
682
683	<	if (states[i] == zcsFixed){
684	<
685	<	zconsMols[i]->getCOMvel(COMvel);
686	<	cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
683	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
684	>	if (states[i] == zcsFixed){
685	>	zconsMols[i]->getCOMvel(COMvel);
686	>	//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
687
688		fixedZAtoms = zconsMols[i]->getMyAtoms();
689	<
690	<	for(int j =0; j < zconsMols[i]->getNAtoms(); j++){
689	>
690	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
691		fixedZAtoms[j]->getVel(vel);
692	<	vel[whichDirection] -= COMvel[whichDirection];
693	<	fixedZAtoms[j]->setVel(vel);
692	>	vel[whichDirection] -= COMvel[whichDirection];
693	>	fixedZAtoms[j]->setVel(vel);
694		}
695
696	<	zconsMols[i]->getCOMvel(COMvel);
697	<	cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
696	>	zconsMols[i]->getCOMvel(COMvel);
697	>	//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl;
698		}
591	–
699		}
700
701	<	cout << "before resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
702	<
701	>	//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl;
702	>
703	>	zSysCOMVel = calcSysCOMVel();
704	>	#ifdef IS_MPI
705	>	if (worldRank == 0){
706	>	#endif
707	>	//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl;
708	>	#ifdef IS_MPI
709	>	}
710	>	#endif
711	>
712		// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules
713		double MVzOfMovingMols_local;
714		double MVzOfMovingMols;
715		double totalMassOfMovingZMols_local;
716		double totalMassOfMovingZMols;
717	<
717	>
718		MVzOfMovingMols_local = 0;
719		totalMassOfMovingZMols_local = 0;
720
721	<	for(int i =0; i < unconsMols.size(); i++){
721	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
722		unconsMols[i]->getCOMvel(COMvel);
723	<	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
723	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
724		}
725
726	<	for(int i = 0; i < zconsMols.size(); i++){
726	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
727		if (states[i] == zcsMoving){
728		zconsMols[i]->getCOMvel(COMvel);
729		MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
730	<	totalMassOfMovingZMols_local += massOfZConsMols[i];
730	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
731		}
616	–
732		}
733
734		#ifndef IS_MPI
735		MVzOfMovingMols = MVzOfMovingMols_local;
736		totalMassOfMovingZMols = totalMassOfMovingZMols_local;
737		#else
738	<	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
739	<	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
738	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
739	>	MPI_SUM, MPI_COMM_WORLD);
740	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
741	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
742		#endif
743
744		double vzOfMovingMols;
745	<	vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
745	>	vzOfMovingMols = MVzOfMovingMols /
746	>	(totalMassOfUncons + totalMassOfMovingZMols);
747
748		//modify the velocites of unconstrained molecules
749		Atom** unconsAtoms;
750	<	for(int i = 0; i < unconsMols.size(); i++){
633	<
750	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
751		unconsAtoms = unconsMols[i]->getMyAtoms();
752	<	for(int j = 0; j < unconsMols[i]->getNAtoms();j++){
752	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
753		unconsAtoms[j]->getVel(vel);
754		vel[whichDirection] -= vzOfMovingMols;
755		unconsAtoms[j]->setVel(vel);
756		}
640	–
757		}
758
759		//modify the velocities of moving z-constrained molecuels
760		Atom** movingZAtoms;
761	<	for(int i = 0; i < zconsMols.size(); i++){
762	<
647	<	if (states[i] ==zcsMoving){
648	<
761	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
762	>	if (states[i] == zcsMoving){
763		movingZAtoms = zconsMols[i]->getMyAtoms();
764	<	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){
764	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
765		movingZAtoms[j]->getVel(vel);
766		vel[whichDirection] -= vzOfMovingMols;
767	<	movingZAtoms[j]->setVel(vel);
768	<	}
769	<
770	<	}
767	>	movingZAtoms[j]->setVel(vel);
768	>	}
769	>	}
770	>	}
771
658	–	}
772
773	<	cout << "after resetting the COMVel of unconstraint molecules is " << calcCOMVel() <<endl;
774	<
773	>	zSysCOMVel = calcSysCOMVel();
774	>	#ifdef IS_MPI
775	>	if (worldRank == 0){
776	>	#endif
777	>	//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl;
778	>	#ifdef IS_MPI
779	>	}
780	>	#endif
781		}
782
783	<	template<typename T> void ZConstraint<T>::doZconstraintForce(){
783	>	/**
784	>	*
785	>	*/
786
787	+	template<typename T> void ZConstraint<T>::doZconstraintForce(){
788		Atom** zconsAtoms;
789		double totalFZ;
790		double totalFZ_local;
669	–	double COMvel[3];
791		double COM[3];
792		double force[3];
793
794	<	int nMovingZMols_local;
674	<	int nMovingZMols;
794	>	//constrain the molecules which do not reach the specified positions
795
676	–	//constrain the molecules which do not reach the specified positions
677	–
796		//Zero Out the force of z-contrained molecules
797		totalFZ_local = 0;
798
799		//calculate the total z-contrained force of fixed z-contrained molecules
800	<	cout << "Fixed Molecules" << endl;
801	<	for(int i = 0; i < zconsMols.size(); i++){
802	<
800	>
801	>	//cout << "before zero out z-constraint force on fixed z-constraint molecuels "
802	>	//       << "total force is " << calcTotalForce() << endl;
803	>
804	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
805		if (states[i] == zcsFixed){
686	–
806		zconsMols[i]->getCOM(COM);
807		zconsAtoms = zconsMols[i]->getMyAtoms();
808
809		fz[i] = 0;
810	<	for(int j =0; j < zconsMols[i]->getNAtoms(); j++) {
810	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
811		zconsAtoms[j]->getFrc(force);
812	<	fz[i] += force[whichDirection];
813	<	}
812	>	fz[i] += force[whichDirection];
813	>	}
814		totalFZ_local += fz[i];
815
816	<	cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
817	<
816	>	//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i]
817	>	//      <<"\tcurrent zpos: " << COM[whichDirection]
818	>	//      << "\tcurrent fz: " <<fz[i] << endl;
819		}
700	–
820		}
821
822	<	//calculate the number of atoms of moving z-constrained molecules
704	<	nMovingZMols_local = 0;
705	<	for(int i = 0; i < zconsMols.size(); i++)
706	<	if(states[i] == zcsMoving)
707	<	nMovingZMols_local += massOfZConsMols[i];
708	<
822	>	//calculate total z-constraint force
823		#ifdef IS_MPI
824	<	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
711	<	MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
824	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
825		#else
826		totalFZ = totalFZ_local;
714	–	nMovingZMols = nMovingZMols_local;
827		#endif
828
717	–	force[0]= 0;
718	–	force[1]= 0;
719	–	force[2]= 0;
720	–	force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols);
829
722	–	//modify the forces of unconstrained molecules
723	–	for(int i = 0; i < unconsMols.size(); i++){
724	–
725	–	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
726	–
727	–	for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)
728	–	unconsAtoms[j]->addFrc(force);
729	–
730	–	}
731	–
732	–	//modify the forces of moving z-constrained molecules
733	–	for(int i = 0; i < zconsMols.size(); i++) {
734	–	if (states[i] == zcsMoving){
735	–
736	–	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
737	–
738	–	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
739	–	movingZAtoms[j]->addFrc(force);
740	–	}
741	–	}
742	–
830		// apply negative to fixed z-constrained molecues;
831	<	force[0]= 0;
832	<	force[1]= 0;
833	<	force[2]= 0;
831	>	force[0] = 0;
832	>	force[1] = 0;
833	>	force[2] = 0;
834
835	<	for(int i = 0; i < zconsMols.size(); i++){
836	<
750	<	if (states[i] == zcsFixed){
751	<
835	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
836	>	if (states[i] == zcsFixed){
837		int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms();
838		zconsAtoms = zconsMols[i]->getMyAtoms();
839	<
840	<	for(int j =0; j < nAtomOfCurZConsMol; j++) {
841	<	force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
839	>
840	>	for (int j = 0; j < nAtomOfCurZConsMol; j++){
841	>	//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol;
842	>	force[whichDirection] = -forcePolicy->getZFOfFixedZMols(zconsMols[i],
843	>	zconsAtoms[j],
844	>	fz[i]);
845		zconsAtoms[j]->addFrc(force);
846		}
759	–
847		}
761	–
848		}
849
850	<	}
850	>	//cout << "after zero out z-constraint force on fixed z-constraint molecuels "
851	>	//      << "total force is " << calcTotalForce() << endl;
852
766	–	template<typename T> bool ZConstraint<T>::checkZConsState(){
767	–	double COM[3];
768	–	double diff;
769	–
770	–	bool changed;
771	–
772	–	changed = false;
773	–
774	–	for(int i =0; i < zconsMols.size(); i++){
853
854	<	zconsMols[i]->getCOM(COM);
855	<	diff = fabs(COM[whichDirection] - zPos[i]);
856	<	if (  diff <= zconsTol && states[i] == zcsMoving){
779	<	states[i] = zcsFixed;
780	<	changed = true;
781	<	}
782	<	else if ( diff > zconsTol && states[i] == zcsFixed){
783	<	states[i] = zcsMoving;
784	<	changed = true;
785	<	}
786	<
787	<	}
854	>	force[0] = 0;
855	>	force[1] = 0;
856	>	force[2] = 0;
857
858	<	return changed;
859	<	}
858	>	//modify the forces of unconstrained molecules
859	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
860	>	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
861
862	<	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
863	<	for(int i = 0; i < zconsMols.size(); i++)
864	<	if (states[i] == zcsFixed)
865	<	return true;
862	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
863	>	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
864	>	force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],
865	>	totalFZ);
866	>	unconsAtoms[j]->addFrc(force);
867	>	}
868	>	}
869
870	<	return false;
871	<	}
870	>	//modify the forces of moving z-constrained molecules
871	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
872	>	if (states[i] == zcsMoving){
873	>	Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
874
875	<
876	<	/**
877	<	*
878	<	*/
879	<	template<typename T> bool ZConstraint<T>::haveMovingZMols(){
880	<	for(int i = 0; i < zconsMols.size(); i++)
881	<	if (states[i] == zcsMoving)
882	<	return true;
883	<
884	<	return false;
810	<
875	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
876	>	//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms);
877	>	force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],
878	>	totalFZ);
879	>	movingZAtoms[j]->addFrc(force);
880	>	}
881	>	}
882	>	}
883	>	//  cout << "after substracting z-constraint force from moving molecuels "
884	>	//        << "total force is " << calcTotalForce()  << endl;
885		}
886
887		/**
#	Line 815 | Line 889 | template<typename T> bool ZConstraint<T>::haveMovingZM
889		*
890		*/
891
892	<	template<typename T> void ZConstraint<T>::doHarmonic(){
892	>	template<typename T> void ZConstraint<T>::doHarmonic(vector<double>& resPos){
893		double force[3];
894		double harmonicU;
895		double harmonicF;
896		double COM[3];
897		double diff;
898	+	double totalFZ_local;
899		double totalFZ;
900	<
900	>
901		force[0] = 0;
902		force[1] = 0;
903		force[2] = 0;
904
905	<	totalFZ = 0;
905	>	totalFZ_local = 0;
906
907	<	cout << "Moving Molecules" << endl;
833	<	for(int i = 0; i < zconsMols.size(); i++) {
834	<
907	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
908		if (states[i] == zcsMoving){
909		zconsMols[i]->getCOM(COM);
910	<	cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl;
911	<
912	<	diff = COM[whichDirection] -zPos[i];
913	<
910	>	//       cout << "Moving Molecule\tindex: " << indexOfZConsMols[i]
911	>	//     << "\tcurrent zpos: " << COM[whichDirection] << endl;
912	>
913	>	diff = COM[whichDirection] - resPos[i];
914	>
915		harmonicU = 0.5 * kz[i] * diff * diff;
916	<	info->lrPot += harmonicU;
916	>	info->lrPot += harmonicU;
917
918	<	harmonicF =  - kz[i] * diff / zconsMols[i]->getNAtoms();
919	<	force[whichDirection] = harmonicF;
920	<	totalFZ += harmonicF;
921	<
918	>	harmonicF = -kz[i] * diff;
919	>	totalFZ_local += harmonicF;
920	>
921	>	//adjust force
922	>
923		Atom** movingZAtoms = zconsMols[i]->getMyAtoms();
924
925	<	for(int j = 0; j < zconsMols[i]->getNAtoms(); j++)
926	<	movingZAtoms[j]->addFrc(force);
925	>	for (int j = 0; j < zconsMols[i]->getNAtoms(); j++){
926	>	//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms();
927	>	force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i],
928	>	movingZAtoms[j],
929	>	harmonicF);
930	>	movingZAtoms[j]->addFrc(force);
931	>	}
932		}
853	–
933		}
934
935	<	force[0]= 0;
936	<	force[1]= 0;
937	<	force[2]= 0;
938	<	force[whichDirection] = -totalFZ /totNumOfUnconsAtoms;
935	>	#ifndef IS_MPI
936	>	totalFZ = totalFZ_local;
937	>	#else
938	>	MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
939	>	#endif
940
941	+	//cout << "before substracting harmonic force from moving molecuels "
942	+	//      << "total force is " << calcTotalForce()  << endl;
943	+
944	+	force[0] = 0;
945	+	force[1] = 0;
946	+	force[2] = 0;
947	+
948		//modify the forces of unconstrained molecules
949	<	for(int i = 0; i < unconsMols.size(); i++){
950	<
951	<	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
952	<
953	<	for(int j = 0; j < unconsMols[i]->getNAtoms(); j++)
954	<	unconsAtoms[j]->addFrc(force);
949	>	for (int i = 0; i < (int) (unconsMols.size()); i++){
950	>	Atom** unconsAtoms = unconsMols[i]->getMyAtoms();
951	>
952	>	for (int j = 0; j < unconsMols[i]->getNAtoms(); j++){
953	>	//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms;
954	>	force[whichDirection] = -forcePolicy->getHFOfUnconsMols(unconsAtoms[j],
955	>	totalFZ);
956	>	unconsAtoms[j]->addFrc(force);
957	>	}
958		}
959
960	+	//cout << "after substracting harmonic force from moving molecuels "
961	+	//      << "total force is " << calcTotalForce()  << endl;
962		}
963
964	<	template<typename T> double ZConstraint<T>::calcCOMVel()
965	<	{
964	>	/**
965	>	*
966	>	*/
967	>
968	>	template<typename T> bool ZConstraint<T>::checkZConsState(){
969	>	double COM[3];
970	>	double diff;
971	>
972	>	int changed_local;
973	>	int changed;
974	>
975	>	changed_local = 0;
976	>
977	>	for (int i = 0; i < (int) (zconsMols.size()); i++){
978	>	zconsMols[i]->getCOM(COM);
979	>	diff = fabs(COM[whichDirection] - zPos[i]);
980	>	if (diff <= zconsTol && states[i] == zcsMoving){
981	>	states[i] = zcsFixed;
982	>	changed_local = 1;
983	>
984	>	if(usingSMD)
985	>	prevCantPos = cantPos;
986	>
987	>	if (hasZConsGap)
988	>	endFixTime[i] = info->getTime() + zconsFixTime;
989	>	}
990	>	else if (diff > zconsTol && states[i] == zcsFixed){
991	>	states[i] = zcsMoving;
992	>	changed_local = 1;
993	>
994	>	if(usingSMD)
995	>	cantPos = prevCantPos;
996	>
997	>	if (hasZConsGap)
998	>	endFixTime[i] = INFINITE_TIME;
999	>	}
1000	>	}
1001	>
1002	>	#ifndef IS_MPI
1003	>	changed = changed_local;
1004	>	#else
1005	>	MPI_Allreduce(&changed_local, &changed, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
1006	>	#endif
1007	>
1008	>	return (changed > 0);
1009	>	}
1010	>
1011	>	template<typename T> bool ZConstraint<T>::haveFixedZMols(){
1012	>	int havingFixed_local;
1013	>	int havingFixed;
1014	>
1015	>	havingFixed_local = 0;
1016	>
1017	>	for (int i = 0; i < (int) (zconsMols.size()); i++)
1018	>	if (states[i] == zcsFixed){
1019	>	havingFixed_local = 1;
1020	>	break;
1021	>	}
1022	>
1023	>	#ifndef IS_MPI
1024	>	havingFixed = havingFixed_local;
1025	>	#else
1026	>	MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT, MPI_SUM,
1027	>	MPI_COMM_WORLD);
1028	>	#endif
1029	>
1030	>	return (havingFixed > 0);
1031	>	}
1032	>
1033	>
1034	>	/**
1035	>	*
1036	>	*/
1037	>	template<typename T> bool ZConstraint<T>::haveMovingZMols(){
1038	>	int havingMoving_local;
1039	>	int havingMoving;
1040	>
1041	>	havingMoving_local = 0;
1042	>
1043	>	for (int i = 0; i < (int) (zconsMols.size()); i++)
1044	>	if (states[i] == zcsMoving){
1045	>	havingMoving_local = 1;
1046	>	break;
1047	>	}
1048	>
1049	>	#ifndef IS_MPI
1050	>	havingMoving = havingMoving_local;
1051	>	#else
1052	>	MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT, MPI_SUM,
1053	>	MPI_COMM_WORLD);
1054	>	#endif
1055	>
1056	>	return (havingMoving > 0);
1057	>	}
1058	>
1059	>	/**
1060	>	*
1061	>	*/
1062	>
1063	>	template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel(){
1064		double MVzOfMovingMols_local;
1065		double MVzOfMovingMols;
1066		double totalMassOfMovingZMols_local;
1067		double totalMassOfMovingZMols;
1068		double COMvel[3];
1069	<
1069	>
1070		MVzOfMovingMols_local = 0;
1071		totalMassOfMovingZMols_local = 0;
1072
1073	<	for(int i =0; i < unconsMols.size(); i++){
1073	>	for (int i = 0; i < unconsMols.size(); i++){
1074		unconsMols[i]->getCOMvel(COMvel);
1075	<	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
1075	>	MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection];
1076		}
1077
1078	<	for(int i = 0; i < zconsMols.size(); i++){
889	<
1078	>	for (int i = 0; i < zconsMols.size(); i++){
1079		if (states[i] == zcsMoving){
1080		zconsMols[i]->getCOMvel(COMvel);
1081		MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection];
1082	<	totalMassOfMovingZMols_local += massOfZConsMols[i];
1082	>	totalMassOfMovingZMols_local += massOfZConsMols[i];
1083		}
895	–
1084		}
1085
1086		#ifndef IS_MPI
1087		MVzOfMovingMols = MVzOfMovingMols_local;
1088		totalMassOfMovingZMols = totalMassOfMovingZMols_local;
1089		#else
1090	<	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1091	<	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD);
1090	>	MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,
1091	>	MPI_SUM, MPI_COMM_WORLD);
1092	>	MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1,
1093	>	MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1094		#endif
1095
1096		double vzOfMovingMols;
1097	<	vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols);
1097	>	vzOfMovingMols = MVzOfMovingMols /
1098	>	(totalMassOfUncons + totalMassOfMovingZMols);
1099
1100		return vzOfMovingMols;
1101		}
1102
1103	+	/**
1104	+	*
1105	+	*/
1106
1107	<	template<typename T> double ZConstraint<T>::calcCOMVel2()
914	<	{
1107	>	template<typename T> double ZConstraint<T>::calcSysCOMVel(){
1108		double COMvel[3];
1109	<	double tempMVz = 0;
1110	<	int index;
1111	<
1112	<	for(int i =0 ; i < nMols; i++){
1113	<	index = isZConstraintMol(&molecules[i]);
1114	<	if( index == -1){
1115	<	molecules[i].getCOMvel(COMvel);
1116	<	tempMVz += molecules[i].getTotalMass()*COMvel[whichDirection];
1109	>	double tempMVz_local;
1110	>	double tempMVz;
1111	>	double massOfZCons_local;
1112	>	double massOfZCons;
1113	>
1114	>
1115	>	tempMVz_local = 0;
1116	>
1117	>	for (int i = 0 ; i < nMols; i++){
1118	>	molecules[i].getCOMvel(COMvel);
1119	>	tempMVz_local += molecules[i].getTotalMass() * COMvel[whichDirection];
1120	>	}
1121	>
1122	>	massOfZCons_local = 0;
1123	>
1124	>	for (int i = 0; i < (int) (massOfZConsMols.size()); i++){
1125	>	massOfZCons_local += massOfZConsMols[i];
1126	>	}
1127	>	#ifndef IS_MPI
1128	>	massOfZCons = massOfZCons_local;
1129	>	tempMVz = tempMVz_local;
1130	>	#else
1131	>	MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE, MPI_SUM,
1132	>	MPI_COMM_WORLD);
1133	>	MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
1134	>	#endif
1135	>
1136	>	return tempMVz / (totalMassOfUncons + massOfZCons);
1137	>	}
1138	>
1139	>	/**
1140	>	*
1141	>	*/
1142	>
1143	>	template<typename T> double ZConstraint<T>::calcTotalForce(){
1144	>	double force[3];
1145	>	double totalForce_local;
1146	>	double totalForce;
1147	>
1148	>	totalForce_local = 0;
1149	>
1150	>	for (int i = 0; i < nAtoms; i++){
1151	>	atoms[i]->getFrc(force);
1152	>	totalForce_local += force[whichDirection];
1153	>	}
1154	>
1155	>	#ifndef IS_MPI
1156	>	totalForce = totalForce_local;
1157	>	#else
1158	>	MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE, MPI_SUM,
1159	>	MPI_COMM_WORLD);
1160	>	#endif
1161	>
1162	>	return totalForce;
1163	>	}
1164	>
1165	>	/**
1166	>	*
1167	>	*/
1168	>
1169	>	template<typename T> void ZConstraint<T>::PolicyByNumber::update(){
1170	>	//calculate the number of atoms of moving z-constrained molecules
1171	>	int nMovingZAtoms_local;
1172	>	int nMovingZAtoms;
1173	>
1174	>	nMovingZAtoms_local = 0;
1175	>	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1176	>	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1177	>	nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms();
1178		}
1179	<	else if(states[i] == zcsMoving){
1180	<	zconsMols[index]->getCOMvel(COMvel);
1181	<	tempMVz += massOfZConsMols[index]*COMvel[whichDirection];
1182	<	}
1179	>
1180	>	#ifdef IS_MPI
1181	>	MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM,
1182	>	MPI_COMM_WORLD);
1183	>	#else
1184	>	nMovingZAtoms = nMovingZAtoms_local;
1185	>	#endif
1186	>	totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms;
1187	>	}
1188	>
1189	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol,
1190	>	Atom* atom,
1191	>	double totalForce){
1192	>	return totalForce / mol->getNAtoms();
1193	>	}
1194	>
1195	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom,
1196	>	double totalForce){
1197	>	return totalForce / totNumOfMovingAtoms;
1198	>	}
1199	>
1200	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol,
1201	>	Atom* atom,
1202	>	double totalForce){
1203	>	return totalForce / mol->getNAtoms();
1204	>	}
1205	>
1206	>	template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom,
1207	>	double totalForce){
1208	>	return totalForce / zconsIntegrator->totNumOfUnconsAtoms;
1209	>	}
1210	>
1211	>	/**
1212	>	*
1213	>	*/
1214	>
1215	>	template<typename T> void ZConstraint<T>::PolicyByMass::update(){
1216	>	//calculate the number of atoms of moving z-constrained molecules
1217	>	double massOfMovingZAtoms_local;
1218	>	double massOfMovingZAtoms;
1219	>
1220	>	massOfMovingZAtoms_local = 0;
1221	>	for (int i = 0; i < (int) ((zconsIntegrator->zconsMols).size()); i++)
1222	>	if ((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)){
1223	>	massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass();
1224	>	}
1225	>
1226	>	#ifdef IS_MPI
1227	>	MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,
1228	>	MPI_SUM, MPI_COMM_WORLD);
1229	>	#else
1230	>	massOfMovingZAtoms = massOfMovingZAtoms_local;
1231	>	#endif
1232	>	totMassOfMovingAtoms = massOfMovingZAtoms +
1233	>	zconsIntegrator->totalMassOfUncons;
1234	>	}
1235	>
1236	>	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol,
1237	>	Atom* atom,
1238	>	double totalForce){
1239	>	return totalForce * atom->getMass() / mol->getTotalMass();
1240	>	}
1241	>
1242	>	template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols(Atom* atom,
1243	>	double totalForce){
1244	>	return totalForce * atom->getMass() / totMassOfMovingAtoms;
1245	>	}
1246	>
1247	>	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol,
1248	>	Atom* atom,
1249	>	double totalForce){
1250	>	return totalForce * atom->getMass() / mol->getTotalMass();
1251	>	}
1252	>
1253	>	template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom,
1254	>	double totalForce){
1255	>	return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons;
1256	>	}
1257	>
1258	>	template<typename T> void ZConstraint<T>::updateZPos(){
1259	>	double curTime;
1260	>	double COM[3];
1261	>
1262	>	curTime = info->getTime();
1263	>
1264	>	for (size_t i = 0; i < zconsMols.size(); i++){
1265	>
1266	>	if (states[i] == zcsFixed && curTime >= endFixTime[i]){
1267	>	zPos[i] += zconsGap;
1268	>
1269	>	if (usingSMD){
1270	>	zconsMols[i]->getCOM(COM);
1271	>	cantPos[i] = COM[whichDirection];
1272	>	}
1273	>
1274	>	}
1275	>
1276		}
1277	<
931	<	return tempMVz /totalMassOfUncons;
1277	>
1278		}
1279	+
1280	+	template<typename T> void ZConstraint<T>::updateCantPos(){
1281	+	double curTime;
1282	+	double dt;
1283	+
1284	+	curTime = info->getTime();
1285	+	dt = info->dt;
1286	+
1287	+	for (size_t i = 0; i < zconsMols.size(); i++){
1288	+	if (states[i] == zcsMoving){
1289	+	cantPos[i] += cantVel[i] * dt;
1290	+	}
1291	+	}
1292	+
1293	+	}

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