Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2018 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "Colvar.h"
23 : #include "core/Atoms.h"
24 : #include "core/PlumedMain.h"
25 : #include "ActionRegister.h"
26 : #include "tools/PDB.h"
27 : #include "tools/RMSD.h"
28 : #include "tools/Tools.h"
29 :
30 : using namespace std;
31 :
32 : namespace PLMD {
33 : namespace colvar {
34 :
35 : class PCARMSD : public Colvar {
36 :
37 : PLMD::RMSD* rmsd;
38 : bool squared;
39 : std::vector< std::vector<Vector> > eigenvectors;
40 : std::vector<PDB> pdbv;
41 : std::vector<string> pca_names;
42 : public:
43 : explicit PCARMSD(const ActionOptions&);
44 : ~PCARMSD();
45 : virtual void calculate();
46 : static void registerKeywords(Keywords& keys);
47 : };
48 :
49 :
50 : using namespace std;
51 :
52 : //+PLUMEDOC DCOLVAR PCARMSD
53 : /*
54 : Calculate the PCA components ( see \cite Sutto:2010 and \cite spiwok ) for a number of provided eigenvectors and an average structure. Performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure.
55 : It takes the average structure and eigenvectors in form of a pdb.
56 : Note that beta and occupancy values in the pdb are neglected and all the weights are placed to 1 (differently from the RMSD colvar for example)
57 :
58 : \par Examples
59 :
60 : \verbatim
61 : PCARMSD AVERAGE=file.pdb EIGENVECTORS=eigenvectors.pdb
62 : \endverbatim
63 :
64 : The input is taken so to be compatible with the output you get from g_covar utility of gromacs (suitably adapted to have a pdb input format).
65 :
66 : */
67 : //+ENDPLUMEDOC
68 :
69 2524 : PLUMED_REGISTER_ACTION(PCARMSD,"PCARMSD")
70 :
71 2 : void PCARMSD::registerKeywords(Keywords& keys) {
72 2 : Colvar::registerKeywords(keys);
73 2 : keys.add("compulsory","AVERAGE","a file in pdb format containing the reference structure and the atoms involved in the CV.");
74 2 : keys.add("compulsory","EIGENVECTORS","a file in pdb format containing the reference structure and the atoms involved in the CV.");
75 : //useCustomisableComponents(keys);
76 2 : keys.addOutputComponent("eig","default","the projections on each eigenvalue are stored on values labeled eig-1, eig-2, ...");
77 2 : keys.addOutputComponent("residual","default","the distance of the present configuration from the configuration supplied as AVERAGE in terms of MSD after optimal alignment ");
78 2 : keys.addFlag("SQUARED-ROOT",false," This should be setted if you want RMSD instead of MSD ");
79 2 : }
80 :
81 1 : PCARMSD::PCARMSD(const ActionOptions&ao):
82 1 : PLUMED_COLVAR_INIT(ao),squared(true)
83 : {
84 1 : string f_average;
85 1 : parse("AVERAGE",f_average);
86 2 : string type;
87 1 : type.assign("OPTIMAL");
88 2 : string f_eigenvectors;
89 1 : parse("EIGENVECTORS",f_eigenvectors);
90 1 : bool sq; parseFlag("SQUARED-ROOT",sq);
91 1 : if (sq) { squared=false; }
92 1 : checkRead();
93 :
94 2 : PDB pdb;
95 :
96 : // read everything in ang and transform to nm if we are not in natural units
97 1 : if( !pdb.read(f_average,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )
98 0 : error("missing input file " + f_average );
99 :
100 1 : rmsd = new RMSD();
101 1 : bool remove_com=true;
102 1 : bool normalize_weights=true;
103 : // here align and displace are a simple vector of ones
104 2 : std::vector<double> align; align=pdb.getOccupancy(); for(unsigned i=0; i<align.size(); i++) {align[i]=1.;} ;
105 2 : std::vector<double> displace; displace=pdb.getBeta(); for(unsigned i=0; i<displace.size(); i++) {displace[i]=1.;} ;
106 : // reset again to reimpose unifrom weights (safe to disable this)
107 1 : rmsd->set(align,displace,pdb.getPositions(),type,remove_com,normalize_weights);
108 1 : requestAtoms( pdb.getAtomNumbers() );
109 :
110 1 : addComponentWithDerivatives("residual"); componentIsNotPeriodic("residual");
111 :
112 1 : log.printf(" average from file %s\n",f_average.c_str());
113 1 : log.printf(" which contains %d atoms\n",getNumberOfAtoms());
114 1 : log.printf(" method for alignment : %s \n",type.c_str() );
115 :
116 1 : log<<" Bibliography "<<plumed.cite("Spiwok, Lipovova and Kralova, JPCB, 111, 3073 (2007) ");
117 1 : log<<" "<<plumed.cite( "Sutto, D'Abramo, Gervasio, JCTC, 6, 3640 (2010)");
118 :
119 : // now get the eigenvectors
120 : // open the file
121 1 : FILE* fp=fopen(f_eigenvectors.c_str(),"r");
122 2 : std::vector<AtomNumber> aaa;
123 : unsigned neigenvects;
124 1 : neigenvects=0;
125 1 : if (fp!=NULL)
126 : {
127 1 : log<<" Opening the eigenvectors file "<<f_eigenvectors.c_str()<<"\n";
128 1 : bool do_read=true;
129 37 : while (do_read) {
130 36 : PDB mypdb;
131 : // check the units for reading this file: how can they make sense?
132 36 : do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());
133 36 : if(do_read) {
134 35 : neigenvects++;
135 35 : if(mypdb.getAtomNumbers().size()==0) error("number of atoms in a frame should be more than zero");
136 35 : unsigned nat=mypdb.getAtomNumbers().size();
137 35 : if(nat!=mypdb.getAtomNumbers().size()) error("frames should have the same number of atoms");
138 35 : if(aaa.empty()) aaa=mypdb.getAtomNumbers();
139 35 : if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
140 35 : log<<" Found eigenvector: "<<neigenvects<<" containing "<<mypdb.getAtomNumbers().size()<<" atoms\n";
141 35 : pdbv.push_back(mypdb);
142 35 : eigenvectors.push_back(mypdb.getPositions());
143 1 : } else {break ;}
144 35 : }
145 1 : fclose (fp);
146 1 : log<<" Found total "<<neigenvects<< " eigenvectors in the file "<<f_eigenvectors.c_str()<<" \n";
147 1 : if(neigenvects==0) error("at least one eigenvector is expected");
148 : }
149 : // the components
150 36 : for(unsigned i=0; i<neigenvects; i++) {
151 35 : std::string num; Tools::convert( i, num );
152 70 : string name; name=string("eig-")+num;
153 35 : pca_names.push_back(name);
154 35 : addComponentWithDerivatives(name); componentIsNotPeriodic(name);
155 35 : }
156 2 : turnOnDerivatives();
157 :
158 1 : }
159 :
160 4 : PCARMSD::~PCARMSD() {
161 1 : delete rmsd;
162 3 : }
163 :
164 :
165 : // calculator
166 546 : void PCARMSD::calculate() {
167 546 : Tensor rotation,invrotation;
168 546 : Matrix<std::vector<Vector> > drotdpos(3,3);
169 1092 : std::vector<Vector> alignedpos;
170 1092 : std::vector<Vector> centeredpos;
171 1092 : std::vector<Vector> centeredref;
172 1092 : std::vector<Vector> ddistdpos;
173 546 : double r=rmsd->calc_PCAelements( getPositions(), ddistdpos, rotation, drotdpos, alignedpos,centeredpos, centeredref,squared);
174 546 : invrotation=rotation.transpose();
175 :
176 546 : Value* verr=getPntrToComponent("residual");
177 546 : verr->set(r);
178 6552 : for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) {
179 6006 : setAtomsDerivatives (verr,iat,ddistdpos[iat]);
180 : }
181 :
182 1092 : std::vector< Vector > der;
183 546 : der.resize(getNumberOfAtoms());
184 :
185 :
186 19656 : for(unsigned i=0; i<eigenvectors.size(); i++) {
187 19110 : Value* value=getPntrToComponent(pca_names[i].c_str());
188 19110 : double val; val=0.;
189 229320 : for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) {
190 210210 : val+=dotProduct(alignedpos[iat]-centeredref[iat],eigenvectors[i][iat]); der[iat].zero();
191 : }
192 19110 : value->set(val);
193 : // here the loop is reversed to better suit the structure of the derivative of the rotation matrix
194 : double tmp1;
195 76440 : for(unsigned a=0; a<3; a++) {
196 229320 : for(unsigned b=0; b<3; b++) {
197 171990 : tmp1=0.;
198 2063880 : for(unsigned n=0; n<getNumberOfAtoms(); n++) {
199 1891890 : tmp1+=centeredpos[n][b]*eigenvectors[i][n][a];
200 : }
201 2063880 : for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) {
202 1891890 : der[iat]+=drotdpos[a][b][iat]*tmp1;
203 : }
204 : }
205 : }
206 19110 : Vector v1;
207 229320 : for(unsigned n=0; n<getNumberOfAtoms(); n++) {
208 210210 : v1+=(1./getNumberOfAtoms())*matmul(invrotation,eigenvectors[i][n]);
209 : }
210 229320 : for(unsigned iat=0; iat<getNumberOfAtoms(); iat++) {
211 210210 : der[iat]+=matmul(invrotation,eigenvectors[i][iat])-v1;
212 210210 : setAtomsDerivatives (value,iat,der[iat]);
213 : }
214 : }
215 :
216 1092 : for(unsigned i=0; i<getNumberOfComponents(); ++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );
217 :
218 546 : }
219 :
220 : }
221 2523 : }
222 :
223 :
224 :
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