applications/staticProps/NitrileFrequencyMap.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 */

#include <algorithm>
#include <fstream>
#include "applications/staticProps/NitrileFrequencyMap.hpp"
#include "utils/simError.h"
#include "io/DumpReader.hpp"
#include "primitives/Molecule.hpp"
#include "brains/Thermo.hpp"

namespace OpenMD {
  
  NitrileFrequencyMap::NitrileFrequencyMap(SimInfo* info, 
                                           const std::string& filename, 
                                           const std::string& sele1, 
                                           int nbins)
    : StaticAnalyser(info, filename), selectionScript1_(sele1), 
      evaluator1_(info), seleMan1_(info), nBins_(nbins), info_(info) {
    
    setOutputName(getPrefix(filename) + ".freqs");
    
    evaluator1_.loadScriptString(sele1);
    if (!evaluator1_.isDynamic()) {
      seleMan1_.setSelectionSet(evaluator1_.evaluate());
    }            
    
    count_.resize(nBins_);
    histogram_.resize(nBins_); 

    freqs_.resize(info_->getNGlobalMolecules());

    minFreq_ = -50;
    maxFreq_ = 50;

    // Values from Choi et. al. "Nitrile and thiocyanate IR probes:
    // Quantum chemistry calculation studies and multivariate
    // least-square ﬁtting analysis," J. Chem. Phys. 128, 134506 (2008).
    //
    // These map site electrostatic potentials onto frequency shifts
    // in the same energy units that one computes the total potential.
    
    frequencyMap_["CN"] = 0.0801;
    frequencyMap_["NC"] = 0.00521;
    frequencyMap_["RCHar3"] = -0.00182;
    frequencyMap_["SigmaN"] = 0.00157;
    frequencyMap_["PiN"] = -0.00167;
    frequencyMap_["PiC"] = -0.00896;

    ForceField* forceField_ = info_->getForceField();
    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
    PairList* excludes = info_->getExcludedInteractions();
    int nAtoms = info->getSnapshotManager()->getCurrentSnapshot()->getNumberOfAtoms();

    RealType rcut;
    if (info_->getSimParams()->haveCutoffRadius()) {
      rcut = info_->getSimParams()->getCutoffRadius();
    } else {
      rcut = 12.0;
    }

    EF_ = V3Zero;

    std::vector<RealType> ef;
    bool efSpec = false;

    if (info_->getSimParams()->haveElectricField()) {
      efSpec = true;
      ef = info_->getSimParams()->getElectricField();            
    }   
    if (info_->getSimParams()->haveUniformField()) {
      efSpec = true;
      ef = info_->getSimParams()->getUniformField();
    }  
    if (efSpec) {
      if (ef.size() != 3) {
        sprintf(painCave.errMsg,
                "NitrileFrequencyMap: Incorrect number of parameters specified for uniformField.\n"
                "\tthere should be 3 parameters, but %lu were specified.\n", ef.size());
        painCave.isFatal = 1;
        simError();      
      }
      EF_.x() = ef[0];
      EF_.y() = ef[1];
      EF_.z() = ef[2];
    }

    excludesForAtom.clear();
    excludesForAtom.resize(nAtoms);

    for (int i = 0; i < nAtoms; i++) {
      for (int j = 0; j < nAtoms; j++) {
        if (excludes->hasPair(i, j)) 
          excludesForAtom[i].push_back(j);              
      }      
    }    

    electrostatic_ = new Electrostatic();
    electrostatic_->setSimInfo(info_);
    electrostatic_->setForceField(forceField_);
    electrostatic_->setSimulatedAtomTypes(atypes);
    electrostatic_->setCutoffRadius(rcut);
  }

  bool NitrileFrequencyMap::excludeAtomPair(int atom1, int atom2) {
    
    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
         i != excludesForAtom[atom1].end(); ++i) {
      if ( (*i) == atom2 ) return true;
    }

    return false;
  }

  void NitrileFrequencyMap::process() {
    Molecule* mol;
    RigidBody* rb;
    Atom* atom;
    AtomType* atype;
    SimInfo::MoleculeIterator mi;
    Molecule::RigidBodyIterator rbIter;
    Molecule::AtomIterator ai2;
    Atom* atom2;
    StuntDouble* sd1;
    int ii, sdID, molID, sdID2;
    RealType li;
    RealType sPot, s1, s2;
    RealType freqShift;
    std::string name;
    map<string,RealType>::iterator fi;
    bool excluded;
    const RealType chrgToKcal = 23.0609;

    DumpReader reader(info_, dumpFilename_);    
    int nFrames = reader.getNFrames();

    nProcessed_ = nFrames/step_;

    std::fill(histogram_.begin(), histogram_.end(), 0.0);
    std::fill(count_.begin(), count_.end(), 0);
    
    for (int istep = 0; istep < nFrames; istep += step_) {
      reader.readFrame(istep);
      currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();

      std::fill(freqs_.begin(), freqs_.end(), 0.0);

      for (mol = info_->beginMolecule(mi); mol != NULL; 
           mol = info_->nextMolecule(mi)) {
        //change the positions of atoms which belong to the rigidbodies
        for (rb = mol->beginRigidBody(rbIter); rb != NULL; 
             rb = mol->nextRigidBody(rbIter)) {
          rb->updateAtoms();
        }
      }     
      
      if  (evaluator1_.isDynamic()) {
        seleMan1_.setSelectionSet(evaluator1_.evaluate());
      }
     
      for (sd1 = seleMan1_.beginSelected(ii);
           sd1 != NULL;
           sd1 = seleMan1_.nextSelected(ii)) {
        
        sdID = sd1->getGlobalIndex();
        molID = info_->getGlobalMolMembership(sdID);
        mol = info_->getMoleculeByGlobalIndex(molID);

        Vector3d CNcentroid = mol->getRigidBodyAt(2)->getPos();
        Vector3d ra = sd1->getPos();

        atom = dynamic_cast<Atom *>(sd1);
        atype = atom->getAtomType();
        name = atype->getName();
        fi = frequencyMap_.find(name);
        if ( fi != frequencyMap_.end() ) {
          li = (*fi).second;
        } else {
          // throw error
          sprintf( painCave.errMsg,
                   "NitrileFrequencyMap::process: Unknown atype requested.\n"
                   "\t(Selection specified %s .)\n",
                   name.c_str() );
          painCave.isFatal = 1;
          simError();
        }

        sPot = sd1->getSitePotential();
        
        // Subtract out the contribution from every other site on this molecule:
        for(atom2 = mol->beginAtom(ai2); atom2 != NULL; 
            atom2 = mol->nextAtom(ai2)) {  

          sdID2 = atom2->getGlobalIndex();
          if (sdID == sdID2) {
            excluded = true;
          } else {
            excluded = excludeAtomPair(sdID, sdID2);
          }

          electrostatic_->getSitePotentials(atom, atom2, excluded, s1, s2); 

          sPot -= s1;
        }

        // Add the contribution from the electric field:

        sPot += dot(EF_, ra - CNcentroid) * chrgToKcal ;

        freqShift = sPot * li;

        // convert the kcal/mol energies to wavenumbers:
        freqShift *= 349.757;

        freqs_[molID] += freqShift;
      }

      for (int i = 0; i < info_->getNGlobalMolecules(); ++i) {
        int binNo = int(nBins_ * (freqs_[i] - minFreq_)/(maxFreq_-minFreq_));

        count_[binNo]++;
      }
    }
      
    processHistogram();
    writeProbs();
    
  }
  
  void NitrileFrequencyMap::processHistogram() {
    
    int atot = 0;
    for(unsigned int i = 0; i < count_.size(); ++i) 
      atot += count_[i];
    
    for(unsigned int i = 0; i < count_.size(); ++i) {
      histogram_[i] = double(count_[i] / double(atot));
    }    
  }
  
  void NitrileFrequencyMap::writeProbs() {

    std::ofstream rdfStream(outputFilename_.c_str());
    if (rdfStream.is_open()) {
      rdfStream << "#NitrileFrequencyMap\n";
      rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
      rdfStream << "#selection1: (" << selectionScript1_ << ")";
      rdfStream << "\n";
      rdfStream << "#nu\tp(nu))\n";
      for (unsigned int i = 0; i < histogram_.size(); ++i) {
        RealType freq = minFreq_ + (RealType)(i)*(maxFreq_-minFreq_) /
          (RealType)histogram_.size();
        rdfStream << freq << "\t" << histogram_[i] << "\n";
      }
      
    } else {
      
      sprintf(painCave.errMsg, "NitrileFrequencyMap: unable to open %s\n", 
              outputFilename_.c_str());
      painCave.isFatal = 1;
      simError();  
    }
    
    rdfStream.close();
  }
  
}

Revision:	2026
Committed:	Wed Oct 22 12:23:59 2014 UTC (10 years, 6 months ago) by gezelter
File size:	10169 byte(s)
Log Message:	Starting to add support for UniformGradient. Changed Vector3d input type to a more general std::vector<RealType> input. This change alters RNEMD and UniformField inputs.
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41	*/
42
43	#include <algorithm>
44	#include <fstream>
45	#include "applications/staticProps/NitrileFrequencyMap.hpp"
46	#include "utils/simError.h"
47	#include "io/DumpReader.hpp"
48	#include "primitives/Molecule.hpp"
49	#include "brains/Thermo.hpp"
50
51	namespace OpenMD {
52
53	NitrileFrequencyMap::NitrileFrequencyMap(SimInfo* info,
54	const std::string& filename,
55	const std::string& sele1,
56	int nbins)
57	: StaticAnalyser(info, filename), selectionScript1_(sele1),
58	evaluator1_(info), seleMan1_(info), nBins_(nbins), info_(info) {
59
60	setOutputName(getPrefix(filename) + ".freqs");
61
62	evaluator1_.loadScriptString(sele1);
63	if (!evaluator1_.isDynamic()) {
64	seleMan1_.setSelectionSet(evaluator1_.evaluate());
65	}
66
67	count_.resize(nBins_);
68	histogram_.resize(nBins_);
69
70	freqs_.resize(info_->getNGlobalMolecules());
71
72	minFreq_ = -50;
73	maxFreq_ = 50;
74
75	// Values from Choi et. al. "Nitrile and thiocyanate IR probes:
76	// Quantum chemistry calculation studies and multivariate
77	// least-square ﬁtting analysis," J. Chem. Phys. 128, 134506 (2008).
78	//
79	// These map site electrostatic potentials onto frequency shifts
80	// in the same energy units that one computes the total potential.
81
82	frequencyMap_["CN"] = 0.0801;
83	frequencyMap_["NC"] = 0.00521;
84	frequencyMap_["RCHar3"] = -0.00182;
85	frequencyMap_["SigmaN"] = 0.00157;
86	frequencyMap_["PiN"] = -0.00167;
87	frequencyMap_["PiC"] = -0.00896;
88
89	ForceField* forceField_ = info_->getForceField();
90	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
91	PairList* excludes = info_->getExcludedInteractions();
92	int nAtoms = info->getSnapshotManager()->getCurrentSnapshot()->getNumberOfAtoms();
93
94	RealType rcut;
95	if (info_->getSimParams()->haveCutoffRadius()) {
96	rcut = info_->getSimParams()->getCutoffRadius();
97	} else {
98	rcut = 12.0;
99	}
100
101	EF_ = V3Zero;
102
103	std::vector<RealType> ef;
104	bool efSpec = false;
105
106	if (info_->getSimParams()->haveElectricField()) {
107	efSpec = true;
108	ef = info_->getSimParams()->getElectricField();
109	}
110	if (info_->getSimParams()->haveUniformField()) {
111	efSpec = true;
112	ef = info_->getSimParams()->getUniformField();
113	}
114	if (efSpec) {
115	if (ef.size() != 3) {
116	sprintf(painCave.errMsg,
117	"NitrileFrequencyMap: Incorrect number of parameters specified for uniformField.\n"
118	"\tthere should be 3 parameters, but %lu were specified.\n", ef.size());
119	painCave.isFatal = 1;
120	simError();
121	}
122	EF_.x() = ef[0];
123	EF_.y() = ef[1];
124	EF_.z() = ef[2];
125	}
126
127	excludesForAtom.clear();
128	excludesForAtom.resize(nAtoms);
129
130	for (int i = 0; i < nAtoms; i++) {
131	for (int j = 0; j < nAtoms; j++) {
132	if (excludes->hasPair(i, j))
133	excludesForAtom[i].push_back(j);
134	}
135	}
136
137	electrostatic_ = new Electrostatic();
138	electrostatic_->setSimInfo(info_);
139	electrostatic_->setForceField(forceField_);
140	electrostatic_->setSimulatedAtomTypes(atypes);
141	electrostatic_->setCutoffRadius(rcut);
142	}
143
144	bool NitrileFrequencyMap::excludeAtomPair(int atom1, int atom2) {
145
146	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
147	i != excludesForAtom[atom1].end(); ++i) {
148	if ( (*i) == atom2 ) return true;
149	}
150
151	return false;
152	}
153
154	void NitrileFrequencyMap::process() {
155	Molecule* mol;
156	RigidBody* rb;
157	Atom* atom;
158	AtomType* atype;
159	SimInfo::MoleculeIterator mi;
160	Molecule::RigidBodyIterator rbIter;
161	Molecule::AtomIterator ai2;
162	Atom* atom2;
163	StuntDouble* sd1;
164	int ii, sdID, molID, sdID2;
165	RealType li;
166	RealType sPot, s1, s2;
167	RealType freqShift;
168	std::string name;
169	map<string,RealType>::iterator fi;
170	bool excluded;
171	const RealType chrgToKcal = 23.0609;
172
173	DumpReader reader(info_, dumpFilename_);
174	int nFrames = reader.getNFrames();
175
176	nProcessed_ = nFrames/step_;
177
178	std::fill(histogram_.begin(), histogram_.end(), 0.0);
179	std::fill(count_.begin(), count_.end(), 0);
180
181	for (int istep = 0; istep < nFrames; istep += step_) {
182	reader.readFrame(istep);
183	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
184
185	std::fill(freqs_.begin(), freqs_.end(), 0.0);
186
187	for (mol = info_->beginMolecule(mi); mol != NULL;
188	mol = info_->nextMolecule(mi)) {
189	//change the positions of atoms which belong to the rigidbodies
190	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
191	rb = mol->nextRigidBody(rbIter)) {
192	rb->updateAtoms();
193	}
194	}
195
196	if (evaluator1_.isDynamic()) {
197	seleMan1_.setSelectionSet(evaluator1_.evaluate());
198	}
199
200	for (sd1 = seleMan1_.beginSelected(ii);
201	sd1 != NULL;
202	sd1 = seleMan1_.nextSelected(ii)) {
203
204	sdID = sd1->getGlobalIndex();
205	molID = info_->getGlobalMolMembership(sdID);
206	mol = info_->getMoleculeByGlobalIndex(molID);
207
208	Vector3d CNcentroid = mol->getRigidBodyAt(2)->getPos();
209	Vector3d ra = sd1->getPos();
210
211	atom = dynamic_cast<Atom *>(sd1);
212	atype = atom->getAtomType();
213	name = atype->getName();
214	fi = frequencyMap_.find(name);
215	if ( fi != frequencyMap_.end() ) {
216	li = (*fi).second;
217	} else {
218	// throw error
219	sprintf( painCave.errMsg,
220	"NitrileFrequencyMap::process: Unknown atype requested.\n"
221	"\t(Selection specified %s .)\n",
222	name.c_str() );
223	painCave.isFatal = 1;
224	simError();
225	}
226
227	sPot = sd1->getSitePotential();
228
229	// Subtract out the contribution from every other site on this molecule:
230	for(atom2 = mol->beginAtom(ai2); atom2 != NULL;
231	atom2 = mol->nextAtom(ai2)) {
232
233	sdID2 = atom2->getGlobalIndex();
234	if (sdID == sdID2) {
235	excluded = true;
236	} else {
237	excluded = excludeAtomPair(sdID, sdID2);
238	}
239
240	electrostatic_->getSitePotentials(atom, atom2, excluded, s1, s2);
241
242	sPot -= s1;
243	}
244
245	// Add the contribution from the electric field:
246
247	sPot += dot(EF_, ra - CNcentroid) * chrgToKcal ;
248
249	freqShift = sPot * li;
250
251	// convert the kcal/mol energies to wavenumbers:
252	freqShift *= 349.757;
253
254	freqs_[molID] += freqShift;
255	}
256
257	for (int i = 0; i < info_->getNGlobalMolecules(); ++i) {
258	int binNo = int(nBins_ * (freqs_[i] - minFreq_)/(maxFreq_-minFreq_));
259
260	count_[binNo]++;
261	}
262	}
263
264	processHistogram();
265	writeProbs();
266
267	}
268
269	void NitrileFrequencyMap::processHistogram() {
270
271	int atot = 0;
272	for(unsigned int i = 0; i < count_.size(); ++i)
273	atot += count_[i];
274
275	for(unsigned int i = 0; i < count_.size(); ++i) {
276	histogram_[i] = double(count_[i] / double(atot));
277	}
278	}
279
280	void NitrileFrequencyMap::writeProbs() {
281
282	std::ofstream rdfStream(outputFilename_.c_str());
283	if (rdfStream.is_open()) {
284	rdfStream << "#NitrileFrequencyMap\n";
285	rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
286	rdfStream << "#selection1: (" << selectionScript1_ << ")";
287	rdfStream << "\n";
288	rdfStream << "#nu\tp(nu))\n";
289	for (unsigned int i = 0; i < histogram_.size(); ++i) {
290	RealType freq = minFreq_ + (RealType)(i)*(maxFreq_-minFreq_) /
291	(RealType)histogram_.size();
292	rdfStream << freq << "\t" << histogram_[i] << "\n";
293	}
294
295	} else {
296
297	sprintf(painCave.errMsg, "NitrileFrequencyMap: unable to open %s\n",
298	outputFilename_.c_str());
299	painCave.isFatal = 1;
300	simError();
301	}
302
303	rdfStream.close();
304	}
305
306	}
307