Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2019 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 "ActionWithArguments.h"
23 : #include "ActionWithValue.h"
24 : #include "tools/PDB.h"
25 : #include "PlumedMain.h"
26 : #include "ActionSet.h"
27 : #include <iostream>
28 : #ifdef __PLUMED_HAS_CREGEX
29 : #include <cstring>
30 : #include <regex.h>
31 : #endif
32 :
33 : using namespace std;
34 : namespace PLMD {
35 :
36 2011 : void ActionWithArguments::registerKeywords(Keywords& keys) {
37 8044 : keys.reserve("numbered","ARG","the input for this action is the scalar output from one or more other actions. The particular scalars that you will use "
38 : "are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates "
39 : "a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the "
40 : "scalars calculated by all the proceding actions in the input file are taken. Some actions have multi-component outputs and "
41 : "each component of the output has a specific label. For example a \\ref DISTANCE action labelled dist may have three componets "
42 : "x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*."
43 : "More information on the referencing of Actions can be found in the section of the manual on the PLUMED \\ref Syntax. "
44 : "Scalar values can also be "
45 : "referenced using POSIX regular expressions as detailed in the section on \\ref Regex. To use this feature you you must compile "
46 : "PLUMED with the appropriate flag.");
47 2011 : }
48 :
49 1957 : void ActionWithArguments::parseArgumentList(const std::string&key,std::vector<Value*>&arg) {
50 3914 : vector<string> c; arg.clear(); parseVector(key,c);
51 5873 : if( c.size()==0 && (keywords.style(key,"compulsory") || keywords.style(key,"hidden")) ) {
52 0 : std::string def; if( keywords.getDefaultValue(key,def) ) c.push_back( def );
53 : }
54 1957 : interpretArgumentList(c,arg);
55 1955 : }
56 :
57 6 : bool ActionWithArguments::parseArgumentList(const std::string&key,int i,std::vector<Value*>&arg) {
58 6 : vector<string> c;
59 : arg.clear();
60 6 : if(parseNumberedVector(key,i,c)) {
61 6 : interpretArgumentList(c,arg);
62 : return true;
63 : } else return false;
64 : }
65 :
66 2057 : void ActionWithArguments::interpretArgumentList(const std::vector<std::string>& c, std::vector<Value*>&arg) {
67 16783 : for(unsigned i=0; i<c.size(); i++) {
68 : // is a regex? then just interpret it. The signal is ()
69 4225 : if(!c[i].compare(0,1,"(")) {
70 189 : unsigned l=c[i].length();
71 189 : if(!c[i].compare(l-1,1,")")) {
72 : // start regex parsing
73 : #ifdef __PLUMED_HAS_CREGEX
74 : // take the string enclosed in quotes and put in round brackets
75 : std::string myregex=c[i];
76 376 : log.printf(" Evaluating regexp for this action: %s \n",myregex.c_str());
77 : int errcode;
78 188 : regex_t *preg = (regex_t*)malloc(sizeof(regex_t)); // pointer to the regular expression
79 : regmatch_t *pmatch;
80 188 : if ((errcode=regcomp(preg, myregex.c_str(),REG_EXTENDED|REG_NEWLINE))) { // compile the regular expression
81 : char* errbuf;
82 : size_t errbuf_size;
83 : // one can check the errors asking to regerror
84 0 : errbuf_size = regerror(errcode, preg, NULL, 0);
85 0 : if (!(errbuf=(char*)malloc(errbuf_size))) {
86 0 : plumed_merror("cannot allocate the buffer for error detection in regexp!");
87 : };
88 0 : regerror(errcode, preg, errbuf, errbuf_size);
89 0 : error(errbuf);
90 : }
91 188 : plumed_massert(preg->re_nsub==1,"I can parse with only one subexpression");
92 188 : pmatch = (regmatch_t*)malloc(sizeof(regmatch_t)*preg->re_nsub);
93 : // select all the actions that have a value
94 376 : std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
95 188 : if( all.empty() ) error("your input file is not telling plumed to calculate anything");
96 2743 : for(unsigned j=0; j<all.size(); j++) {
97 1578 : std::vector<std::string> ss=all[j]->getComponentsVector();
98 635463 : for(unsigned k=0; k<ss.size(); ++k) {
99 211295 : unsigned ll=strlen(ss[k].c_str())+1;
100 211295 : std::vector<char> str(ll);
101 : strcpy(&str[0],ss[k].c_str());
102 : const char *ppstr=&str[0];
103 211295 : if(!regexec(preg, ppstr, preg->re_nsub, pmatch, 0)) {
104 53926 : log.printf(" Something matched with \"%s\" : ",ss[k].c_str());
105 : do {
106 26963 : if (pmatch[0].rm_so != -1) { /* The regex is matching part of a string */
107 : char *submatch;
108 26963 : size_t matchlen = pmatch[0].rm_eo - pmatch[0].rm_so;
109 26963 : submatch = (char*)malloc(matchlen+1);
110 26963 : strncpy(submatch, ppstr+pmatch[0].rm_so, matchlen+1);
111 26963 : submatch[matchlen]='\0';
112 26963 : log.printf(" subpattern %s\n", submatch);
113 : // this is the match: try to see if it is a valid action
114 26963 : std::string putativeVal(submatch);
115 26963 : if( all[j]->exists(putativeVal) ) {
116 40952 : arg.push_back(all[j]->copyOutput(putativeVal));
117 40952 : log.printf(" Action %s added! \n",putativeVal.c_str());
118 : }
119 26963 : free(submatch);
120 : };
121 26963 : ppstr += pmatch[0].rm_eo; /* Restart from last match */
122 26963 : } while(!regexec(preg,ppstr,preg->re_nsub,pmatch,0));
123 : }
124 : }
125 : };
126 188 : regfree(preg);
127 188 : free(preg);
128 188 : free(pmatch);
129 : #else
130 : plumed_merror("Regexp support not compiled!");
131 : #endif
132 : } else {
133 4 : plumed_merror("did you want to use regexp to input arguments? enclose it between two round braces (...) with no spaces!");
134 : }
135 : } else {
136 : std::size_t dot=c[i].find_first_of('.');
137 4036 : string a=c[i].substr(0,dot);
138 4036 : string name=c[i].substr(dot+1);
139 4036 : if(c[i].find(".")!=string::npos) { // if it contains a dot:
140 1435 : if(a=="*" && name=="*") {
141 : // Take all values from all actions
142 2 : std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
143 1 : if( all.empty() ) error("your input file is not telling plumed to calculate anything");
144 26 : for(unsigned j=0; j<all.size(); j++) {
145 46 : for(int k=0; k<all[j]->getNumberOfComponents(); ++k) arg.push_back(all[j]->copyOutput(k));
146 : }
147 1426 : } else if ( name=="*") {
148 : // Take all the values from an action with a specific name
149 876 : ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
150 438 : if(!action) {
151 1 : std::string str=" (hint! the actions with value in this ActionSet are: ";
152 0 : str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
153 0 : error("cannot find action named " + a + str);
154 : }
155 439 : if( action->getNumberOfComponents()==0 ) error("found " + a +".* indicating use all components calculated by action with label " + a + " but this action has no components");
156 9677 : for(int k=0; k<action->getNumberOfComponents(); ++k) arg.push_back(action->copyOutput(k));
157 988 : } else if ( a=="*" ) {
158 : // Take components from all actions with a specific name
159 14 : std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
160 7 : if( all.empty() ) error("your input file is not telling plumed to calculate anything");
161 : unsigned nval=0;
162 86 : for(unsigned j=0; j<all.size(); j++) {
163 96 : std::string flab; flab=all[j]->getLabel() + "." + name;
164 42 : if( all[j]->exists(flab) ) { arg.push_back(all[j]->copyOutput(flab)); nval++; }
165 : }
166 7 : if(nval==0) error("found no actions with a component called " + name );
167 : } else {
168 : // Take values with a specific name
169 1962 : ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(a);
170 981 : if(!action) {
171 1 : std::string str=" (hint! the actions with value in this ActionSet are: ";
172 0 : str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
173 0 : error("cannot find action named " + a +str);
174 : }
175 981 : if( !(action->exists(c[i])) ) {
176 1 : std::string str=" (hint! the components in this actions are: ";
177 0 : str+=action->getComponentsList()+")";
178 0 : error("action " + a + " has no component named " + name + str);
179 : } ;
180 1963 : arg.push_back(action->copyOutput(c[i]));
181 : }
182 : } else { // if it doesn't contain a dot
183 2609 : if(c[i]=="*") {
184 : // Take all values from all actions
185 120 : std::vector<ActionWithValue*> all=plumed.getActionSet().select<ActionWithValue*>();
186 60 : if( all.empty() ) error("your input file is not telling plumed to calculate anything");
187 1218 : for(unsigned j=0; j<all.size(); j++) {
188 2118 : for(int k=0; k<all[j]->getNumberOfComponents(); ++k) arg.push_back(all[j]->copyOutput(k));
189 : }
190 : } else {
191 5098 : ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(c[i]);
192 2549 : if(!action) {
193 2 : std::string str=" (hint! the actions with value in this ActionSet are: ";
194 5 : str+=plumed.getActionSet().getLabelList<ActionWithValue*>()+")";
195 4 : error("cannot find action named " + c[i] + str );
196 : }
197 2548 : if( !(action->exists(c[i])) ) {
198 1 : std::string str=" (hint! the components in this actions are: ";
199 0 : str+=action->getComponentsList()+")";
200 0 : error("action " + c[i] + " has no component named " + c[i] +str);
201 : };
202 5097 : arg.push_back(action->copyOutput(c[i]));
203 : }
204 : }
205 : }
206 : }
207 2055 : }
208 :
209 442 : void ActionWithArguments::expandArgKeywordInPDB( PDB& pdb ) {
210 884 : std::vector<std::string> pdb_remark=pdb.getRemark();
211 442 : std::vector<std::string> arg_names;
212 884 : bool found=Tools::parseVector(pdb_remark,"ARG",arg_names);
213 442 : if( found ) {
214 : std::vector<Value*> arg_vals;
215 80 : interpretArgumentList( arg_names, arg_vals );
216 160 : std::string new_args="ARG=" + arg_vals[0]->getName();
217 640 : for(unsigned i=1; i<arg_vals.size(); ++i) new_args = new_args + "," + arg_vals[i]->getName();
218 80 : pdb.setArgKeyword( new_args );
219 : }
220 442 : }
221 :
222 3052 : void ActionWithArguments::requestArguments(const vector<Value*> &arg) {
223 3052 : plumed_massert(!lockRequestArguments,"requested argument list can only be changed in the prepare() method");
224 3052 : arguments=arg;
225 3052 : clearDependencies();
226 : std::string fullname,name;
227 76835 : for(unsigned i=0; i<arguments.size(); i++) {
228 23577 : fullname=arguments[i]->getName();
229 23577 : if(fullname.find(".")!=string::npos) {
230 : std::size_t dot=fullname.find_first_of('.');
231 35684 : name=fullname.substr(0,dot);
232 : } else {
233 : name=fullname;
234 : }
235 47154 : ActionWithValue* action=plumed.getActionSet().selectWithLabel<ActionWithValue*>(name);
236 23577 : plumed_massert(action,"cannot find action named (in requestArguments - this is weird)" + name);
237 23577 : addDependency(action);
238 : }
239 3052 : }
240 :
241 1950 : ActionWithArguments::ActionWithArguments(const ActionOptions&ao):
242 : Action(ao),
243 3900 : lockRequestArguments(false)
244 : {
245 5852 : if( keywords.exists("ARG") && !keywords.exists("DATA") ) {
246 : vector<Value*> arg;
247 3766 : parseArgumentList("ARG",arg);
248 :
249 1881 : if(!arg.empty()) {
250 1824 : log.printf(" with arguments");
251 86236 : for(unsigned i=0; i<arg.size(); i++) log.printf(" %s",arg[i]->getName().c_str());
252 1824 : log.printf("\n");
253 : }
254 1881 : requestArguments(arg);
255 : }
256 1948 : }
257 :
258 58 : void ActionWithArguments::calculateNumericalDerivatives( ActionWithValue* a ) {
259 58 : if(!a) {
260 58 : a=dynamic_cast<ActionWithValue*>(this);
261 58 : plumed_massert(a,"cannot compute numerical derivatives for an action without values");
262 : }
263 :
264 : const int nval=a->getNumberOfComponents();
265 58 : const int npar=arguments.size();
266 58 : std::vector<double> value (nval*npar);
267 264 : for(int i=0; i<npar; i++) {
268 206 : double arg0=arguments[i]->get();
269 103 : arguments[i]->set(arg0+sqrt(epsilon));
270 103 : a->calculate();
271 103 : arguments[i]->set(arg0);
272 2535 : for(int j=0; j<nval; j++) {
273 2432 : value[i*nval+j]=a->getOutputQuantity(j);
274 : }
275 : }
276 58 : a->calculate();
277 58 : a->clearDerivatives();
278 2230 : for(int j=0; j<nval; j++) {
279 1086 : Value* v=a->copyOutput(j);
280 1886 : if( v->hasDerivatives() ) for(int i=0; i<npar; i++) v->addDerivative(i,(value[i*nval+j]-a->getOutputQuantity(j))/sqrt(epsilon));
281 : }
282 58 : }
283 :
284 261 : double ActionWithArguments::getProjection(unsigned i,unsigned j)const {
285 522 : plumed_massert(i<arguments.size()," making projections with an index which is too large");
286 261 : plumed_massert(j<arguments.size()," making projections with an index which is too large");
287 261 : const Value* v1=arguments[i];
288 261 : const Value* v2=arguments[j];
289 261 : return Value::projection(*v1,*v2);
290 : }
291 :
292 326 : void ActionWithArguments::addForcesOnArguments( const std::vector<double>& forces ) {
293 1152 : for(unsigned i=0; i<arguments.size(); ++i) arguments[i]->addForce( forces[i] );
294 326 : }
295 :
296 4839 : }
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