Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2012-2019 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 "Keywords.h"
23 : #include "Log.h"
24 : #include "Tools.h"
25 : #include <iostream>
26 :
27 : namespace PLMD {
28 :
29 495810 : Keywords::KeyType::KeyType( const std::string& type ) {
30 495810 : if( type=="compulsory" ) {
31 131942 : style=compulsory;
32 363868 : } else if( type=="flag" ) {
33 93810 : style=flag;
34 270058 : } else if( type=="optional" ) {
35 139626 : style=optional;
36 130432 : } else if( type.find("atoms")!=std::string::npos || type.find("residues")!=std::string::npos ) {
37 66436 : style=atoms;
38 63996 : } else if( type=="hidden" ) {
39 30710 : style=hidden;
40 33286 : } else if( type=="vessel" ) {
41 33286 : style=vessel;
42 : } else {
43 0 : plumed_massert(false,"invalid keyword specifier " + type);
44 : }
45 495810 : }
46 :
47 2369 : void Keywords::KeyType::setStyle( const std::string& type ) {
48 2369 : if( type=="compulsory" ) {
49 66 : style=compulsory;
50 2303 : } else if( type=="flag" ) {
51 0 : style=flag;
52 2303 : } else if( type=="optional" ) {
53 25 : style=optional;
54 2278 : } else if( type.find("atoms")!=std::string::npos || type.find("residues")!=std::string::npos ) {
55 191 : style=atoms;
56 2087 : } else if( type=="hidden" ) {
57 129 : style=hidden;
58 1958 : } else if( type=="vessel" ) {
59 1958 : style=vessel;
60 : } else {
61 0 : plumed_massert(false,"invalid keyword specifier " + type);
62 : }
63 2369 : }
64 :
65 662 : void Keywords::add( const Keywords& newkeys ) {
66 662 : newkeys.copyData( keys, reserved_keys, types, allowmultiple, documentation, booldefs, numdefs, atomtags, cnames, ckey, cdocs );
67 662 : }
68 :
69 662 : void Keywords::copyData( std::vector<std::string>& kk, std::vector<std::string>& rk, std::map<std::string,KeyType>& tt, std::map<std::string,bool>& am,
70 : std::map<std::string,std::string>& docs, std::map<std::string,bool>& bools, std::map<std::string,std::string>& nums,
71 : std::map<std::string,std::string>& atags, std::vector<std::string>& cnam, std::map<std::string,std::string>& ck,
72 : std::map<std::string,std::string>& cd ) const {
73 1324 : for(unsigned i=0; i<keys.size(); ++i) {
74 0 : std::string thiskey=keys[i];
75 0 : for(unsigned j=0; j<kk.size(); ++j) plumed_massert( thiskey!=kk[j], "keyword " + thiskey + " is in twice" );
76 0 : for(unsigned j=0; j<rk.size(); ++j) plumed_massert( thiskey!=rk[j], "keyword " + thiskey + " is in twice" );
77 0 : kk.push_back( thiskey );
78 0 : plumed_massert( types.count( thiskey ), "no type data on keyword " + thiskey + " to copy" );
79 0 : tt.insert( std::pair<std::string,KeyType>( thiskey,types.find(thiskey)->second) );
80 0 : if( (types.find(thiskey)->second).isAtomList() ) atags.insert( std::pair<std::string,std::string>( thiskey,atomtags.find(thiskey)->second) );
81 0 : plumed_massert( allowmultiple.count( thiskey ), "no numbered data on keyword " + thiskey + " to copy" );
82 0 : am.insert( std::pair<std::string,bool>(thiskey,allowmultiple.find(thiskey)->second) );
83 0 : plumed_massert( documentation.count( thiskey ), "no documentation for keyword " + thiskey + " to copy" );
84 0 : docs.insert( std::pair<std::string,std::string>(thiskey,documentation.find(thiskey)->second) );
85 0 : if( booldefs.count( thiskey ) ) bools.insert( std::pair<std::string,bool>( thiskey,booldefs.find(thiskey)->second) );
86 0 : if( numdefs.count( thiskey ) ) nums.insert( std::pair<std::string,std::string>( thiskey,numdefs.find(thiskey)->second) );
87 : }
88 24494 : for(unsigned i=0; i<reserved_keys.size(); ++i) {
89 11916 : std::string thiskey=reserved_keys[i];
90 198072 : for(unsigned j=0; j<kk.size(); ++j) plumed_massert( thiskey!=kk[j], "keyword " + thiskey + " is in twice" );
91 318600 : for(unsigned j=0; j<rk.size(); ++j) plumed_massert( thiskey!=rk[j], "keyword " + thiskey + " is in twice" );
92 11916 : rk.push_back( thiskey );
93 11916 : plumed_massert( types.count( thiskey ), "no type data on keyword " + thiskey + " to copy" );
94 11916 : tt.insert( std::pair<std::string,KeyType>( thiskey,types.find(thiskey)->second) );
95 11916 : if( (types.find(thiskey)->second).isAtomList() ) atags.insert( std::pair<std::string,std::string>( thiskey,atomtags.find(thiskey)->second) );
96 11916 : plumed_massert( allowmultiple.count( thiskey ), "no numbered data on keyword " + thiskey + " to copy" );
97 11916 : am.insert( std::pair<std::string,bool>(thiskey,allowmultiple.find(thiskey)->second) );
98 11916 : plumed_massert( documentation.count( thiskey ), "no documentation for keyword " + thiskey + " to copy" );
99 23832 : docs.insert( std::pair<std::string,std::string>(thiskey,documentation.find(thiskey)->second) );
100 11916 : if( booldefs.count( thiskey ) ) bools.insert( std::pair<std::string,bool>( thiskey,booldefs.find(thiskey)->second) );
101 11916 : if( numdefs.count( thiskey ) ) nums.insert( std::pair<std::string,std::string>( thiskey,numdefs.find(thiskey)->second) );
102 : }
103 24494 : for(unsigned i=0; i<cnames.size(); ++i) {
104 11916 : std::string thisnam=cnames[i];
105 214488 : for(unsigned j=0; j<cnam.size(); ++j) plumed_massert( thisnam!=cnam[j], "component " + thisnam + " is in twice" );
106 11916 : cnam.push_back( thisnam );
107 11916 : plumed_massert( ckey.count( thisnam ), "no keyword data on component " + thisnam + " to copy" );
108 23832 : ck.insert( std::pair<std::string,std::string>( thisnam, ckey.find(thisnam)->second) );
109 11916 : plumed_massert( cdocs.count( thisnam ), "no documentation on component " + thisnam + " to copy" );
110 23832 : cd.insert( std::pair<std::string,std::string>( thisnam, cdocs.find(thisnam)->second) );
111 : }
112 662 : }
113 :
114 61303 : void Keywords::reserve( const std::string & t, const std::string & k, const std::string & d ) {
115 61303 : plumed_assert( !exists(k) && !reserved(k) );
116 61303 : std::string fd, lowkey=k;
117 : // Convert to lower case
118 122606 : std::transform(lowkey.begin(),lowkey.end(),lowkey.begin(),tolower);
119 : // Remove any underscore characters
120 : for(unsigned i=0;; ++i) {
121 83029 : std::size_t num=lowkey.find_first_of("_");
122 83029 : if( num==std::string::npos ) break;
123 21726 : lowkey.erase( lowkey.begin() + num, lowkey.begin() + num + 1 );
124 : }
125 61303 : if( t=="vessel" ) {
126 99858 : fd = d + " The final value can be referenced using <em>label</em>." + lowkey;
127 62656 : if(d.find("flag")==std::string::npos) fd += ". You can use multiple instances of this keyword i.e. " +
128 146850 : k +"1, " + k + "2, " + k + "3... The corresponding values are then "
129 117480 : "referenced using <em>label</em>."+ lowkey +"-1, <em>label</em>." + lowkey +
130 58740 : "-2, <em>label</em>." + lowkey + "-3...";
131 33286 : allowmultiple.insert( std::pair<std::string,bool>(k,true) );
132 99858 : types.insert( std::pair<std::string,KeyType>(k,KeyType("vessel")) );
133 28017 : } else if( t=="numbered" ) {
134 20920 : fd = d + " You can use multiple instances of this keyword i.e. " + k +"1, " + k + "2, " + k + "3...";
135 2615 : allowmultiple.insert( std::pair<std::string,bool>(k,true) );
136 7845 : types.insert( std::pair<std::string,KeyType>(k,KeyType("optional")) );
137 : } else {
138 : fd = d;
139 25402 : if( t=="atoms" && isaction ) fd = d + ". For more information on how to specify lists of atoms see \\ref Group";
140 25402 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
141 50804 : types.insert( std::pair<std::string,KeyType>(k,KeyType(t)) );
142 26644 : if( (types.find(k)->second).isAtomList() ) atomtags.insert( std::pair<std::string,std::string>(k,t) );
143 : }
144 122606 : documentation.insert( std::pair<std::string,std::string>(k,fd) );
145 61303 : reserved_keys.push_back(k);
146 61303 : }
147 :
148 1890 : void Keywords::reserveFlag( const std::string & k, const bool def, const std::string & d ) {
149 1890 : plumed_assert( !exists(k) && !reserved(k) );
150 : std::string defstr;
151 1890 : if( def ) { defstr="( default=on ) "; } else { defstr="( default=off ) "; }
152 5670 : types.insert( std::pair<std::string,KeyType>(k,KeyType("flag")) );
153 5670 : std::string fd,lowkey=k; std::transform(lowkey.begin(),lowkey.end(),lowkey.begin(),tolower);
154 3780 : fd=defstr + d;
155 3780 : documentation.insert( std::pair<std::string,std::string>(k,fd) );
156 1890 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
157 1890 : booldefs.insert( std::pair<std::string,bool>(k,def) );
158 1890 : reserved_keys.push_back(k);
159 1890 : }
160 :
161 12937 : void Keywords::use( const std::string & k ) {
162 12937 : plumed_massert( reserved(k), "the " + k + " keyword is not reserved");
163 325219 : for(unsigned i=0; i<reserved_keys.size(); ++i) {
164 156141 : if(reserved_keys[i]==k) keys.push_back( reserved_keys[i] );
165 : }
166 12937 : }
167 :
168 2369 : void Keywords::reset_style( const std::string & k, const std::string & style ) {
169 2369 : plumed_massert( exists(k) || reserved(k), "no " + k + " keyword" );
170 2369 : (types.find(k)->second).setStyle(style);
171 2369 : if( (types.find(k)->second).isVessel() ) allowmultiple[k]=true;
172 2560 : if( (types.find(k)->second).isAtomList() ) atomtags.insert( std::pair<std::string,std::string>(k,style) );
173 2369 : }
174 :
175 240863 : void Keywords::add( const std::string & t, const std::string & k, const std::string & d ) {
176 722589 : plumed_massert( !exists(k) && t!="flag" && !reserved(k) && t!="vessel", "keyword " + k + " has already been registered");
177 : std::string fd;
178 240863 : if( t=="numbered" ) {
179 10272 : fd=d + " You can use multiple instances of this keyword i.e. " + k +"1, " + k + "2, " + k + "3...";
180 1284 : allowmultiple.insert( std::pair<std::string,bool>(k,true) );
181 3852 : types.insert( std::pair<std::string,KeyType>(k, KeyType("optional")) );
182 : } else {
183 : fd=d;
184 239579 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
185 479158 : types.insert( std::pair<std::string,KeyType>(k,KeyType(t)) );
186 304773 : if( (types.find(k)->second).isAtomList() ) atomtags.insert( std::pair<std::string,std::string>(k,t) );
187 : }
188 246680 : if( t=="atoms" && isaction ) fd = d + ". For more information on how to specify lists of atoms see \\ref Group";
189 481726 : documentation.insert( std::pair<std::string,std::string>(k,fd) );
190 240863 : keys.push_back(k);
191 240863 : }
192 :
193 99834 : void Keywords::add( const std::string & t, const std::string & k, const std::string & def, const std::string & d ) {
194 199668 : plumed_assert( !exists(k) && !reserved(k) && (t=="compulsory" || t=="hidden" )); // An optional keyword can't have a default
195 199668 : types.insert( std::pair<std::string,KeyType>(k, KeyType(t)) );
196 399336 : documentation.insert( std::pair<std::string,std::string>(k,"( default=" + def + " ) " + d) );
197 99834 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
198 199668 : numdefs.insert( std::pair<std::string,std::string>(k,def) );
199 99834 : keys.push_back(k);
200 99834 : }
201 :
202 91920 : void Keywords::addFlag( const std::string & k, const bool def, const std::string & d ) {
203 91920 : plumed_massert( !exists(k) && !reserved(k), "keyword " + k + " has already been registered");
204 : std::string defstr;
205 91920 : if( def ) { defstr="( default=on ) "; } else { defstr="( default=off ) "; }
206 275760 : types.insert( std::pair<std::string,KeyType>(k,KeyType("flag")) );
207 275760 : documentation.insert( std::pair<std::string,std::string>(k,defstr + d) );
208 91920 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
209 91920 : booldefs.insert( std::pair<std::string,bool>(k,def) );
210 91920 : keys.push_back(k);
211 91920 : }
212 :
213 1239 : void Keywords::remove( const std::string & k ) {
214 : bool found=false; unsigned j=0, n=0;
215 :
216 : while(true) {
217 24300 : for(j=0; j<keys.size(); j++) if(keys[j]==k)break;
218 57605 : for(n=0; n<reserved_keys.size(); n++) if(reserved_keys[n]==k)break;
219 2478 : if(j<keys.size()) {
220 2432 : keys.erase(keys.begin()+j);
221 : found=true;
222 1262 : } else if(n<reserved_keys.size()) {
223 46 : reserved_keys.erase(reserved_keys.begin()+n);
224 : found=true;
225 : } else break;
226 : }
227 : // Delete documentation, type and so on from the description
228 : types.erase(k); documentation.erase(k); allowmultiple.erase(k); booldefs.erase(k); numdefs.erase(k);
229 1239 : plumed_massert(found,"You are trying to forbid " + k + " a keyword that isn't there"); // You have tried to forbid a keyword that isn't there
230 1239 : }
231 :
232 7840 : bool Keywords::numbered( const std::string & k ) const {
233 15680 : if( style( k,"atoms") ) return true;
234 5902 : plumed_massert( allowmultiple.count(k), "Did not find keyword " + k );
235 5902 : return allowmultiple.find(k)->second;
236 : }
237 :
238 503646 : bool Keywords::style( const std::string & k, const std::string & t ) const {
239 503646 : plumed_massert( types.count(k), "Did not find keyword " + k );
240 :
241 1007292 : if( (types.find(k)->second).toString()==t ) return true;
242 392068 : return false;
243 : }
244 :
245 643035 : unsigned Keywords::size() const {
246 643035 : return keys.size();
247 : }
248 :
249 8964 : std::string Keywords::getKeyword( const unsigned i ) const {
250 8964 : plumed_assert( i<size() );
251 17928 : return keys[i];
252 : }
253 :
254 644199 : bool Keywords::exists( const std::string & k ) const {
255 14272560 : for(unsigned i=0; i<keys.size(); ++i) {
256 6619997 : if( keys[i]==k ) return true;
257 : }
258 : return false;
259 : }
260 :
261 510825 : bool Keywords::reserved( const std::string & k ) const {
262 2629888 : for(unsigned i=0; i<reserved_keys.size(); ++i) {
263 819134 : if( reserved_keys[i]==k ) return true;
264 : }
265 : return false;
266 : }
267 :
268 0 : void Keywords::print_template(const std::string& actionname, bool include_optional) const {
269 : unsigned nkeys=0;
270 : printf("%s",actionname.c_str());
271 0 : for(unsigned i=0; i<keys.size(); ++i) {
272 0 : if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
273 : }
274 0 : if( nkeys>0 ) {
275 0 : std::string prevtag="start";
276 0 : for(unsigned i=0; i<keys.size(); ++i) {
277 0 : if( (types.find(keys[i])->second).isAtomList() ) {
278 0 : plumed_massert( atomtags.count(keys[i]), "keyword " + keys[i] + " allegedly specifies atoms but no tag has been specified. Please email Gareth Tribello");
279 0 : if( prevtag!="start" && prevtag!=atomtags.find(keys[i])->second ) break;
280 0 : if( (atomtags.find(keys[i])->second).find("residues")!=std::string::npos) printf(" %s=<residue selection>", keys[i].c_str() );
281 : else printf(" %s=<atom selection>", keys[i].c_str() );
282 0 : prevtag=atomtags.find(keys[i])->second;
283 : }
284 : }
285 : }
286 : nkeys=0;
287 0 : for(unsigned i=0; i<keys.size(); ++i) {
288 0 : if ( include_optional || \
289 0 : (types.find(keys[i])->second).isCompulsory() ) nkeys++;
290 : }
291 0 : if( nkeys>0 ) {
292 0 : for(unsigned i=0; i<keys.size(); ++i) {
293 0 : if ( (types.find(keys[i])->second).isCompulsory() ) {
294 : std::string def;
295 0 : if( getDefaultValue( keys[i], def) ) {
296 : printf(" %s=%s ", keys[i].c_str(), def.c_str() );
297 : } else {
298 : printf(" %s= ", keys[i].c_str() );
299 : }
300 0 : } else if (include_optional) {
301 : // TG no defaults for optional keywords?
302 : printf(" [%s]", keys[i].c_str() );
303 : }
304 : }
305 : }
306 : printf("\n");
307 0 : }
308 :
309 270 : void Keywords::print_vim() const {
310 8186 : for(unsigned i=0; i<keys.size(); ++i) {
311 3823 : if( (types.find(keys[i])->second).isFlag() ) {
312 : printf( ",flag:%s", keys[i].c_str() );
313 : } else {
314 2971 : if( allowmultiple.find(keys[i])->second ) printf(",numbered:%s",keys[i].c_str() );
315 : else printf(",option:%s",keys[i].c_str() );
316 : }
317 : }
318 270 : fprintf(stdout,"\n");
319 270 : print(stdout);
320 270 : }
321 :
322 0 : void Keywords::print_html() const {
323 :
324 : // This is the part that outputs the details of the components
325 0 : if( cnames.size()>0 ) {
326 : unsigned ndef=0;
327 0 : for(unsigned i=0; i<cnames.size(); ++i) {
328 0 : if(ckey.find(cnames[i])->second=="default") ndef++;
329 : }
330 :
331 0 : if( ndef>0 ) {
332 0 : std::cout<<"\\par Description of components\n\n";
333 0 : std::cout<<cstring<<"\n\n";
334 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
335 : printf("<tr> <td width=5%%> <b> Quantity </b> </td> <td> <b> Description </b> </td> </tr>\n");
336 : unsigned nndef=0;
337 0 : for(unsigned i=0; i<cnames.size(); ++i) {
338 : //plumed_assert( ckey.find(cnames[i])->second=="default" );
339 0 : if( ckey.find(cnames[i])->second!="default" ) { nndef++; continue; }
340 : printf("<tr>\n");
341 : printf("<td width=15%%> <b> %s </b></td>\n",cnames[i].c_str() );
342 : printf("<td> %s </td>\n",(cdocs.find(cnames[i])->second).c_str() );
343 : printf("</tr>\n");
344 : }
345 0 : std::cout<<"</table>\n\n";
346 0 : if( nndef>0 ) {
347 0 : std::cout<<"In addition the following quantities can be calculated by employing the keywords listed below"<<std::endl;
348 0 : std::cout<<"\n\n";
349 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
350 : printf("<tr> <td width=5%%> <b> Quantity </b> </td> <td> <b> Keyword </b> </td> <td> <b> Description </b> </td> </tr>\n");
351 0 : for(unsigned i=0; i<cnames.size(); ++i) {
352 0 : if( ckey.find(cnames[i])->second!="default") {
353 : printf("<tr>\n");
354 : printf("<td width=5%%> <b> %s </b></td> <td width=10%%> <b> %s </b> </td> \n",
355 : cnames[i].c_str(),(ckey.find(cnames[i])->second).c_str() );
356 : printf("<td> %s </td>\n",(cdocs.find(cnames[i])->second).c_str() );
357 : printf("</tr>\n");
358 : }
359 : }
360 0 : std::cout<<"</table>\n\n";
361 : }
362 : } else {
363 : unsigned nregs=0;
364 0 : for(unsigned i=0; i<cnames.size(); ++i) {
365 0 : if( exists(ckey.find(cnames[i])->second) ) nregs++;
366 : }
367 0 : if( nregs>0 ) {
368 0 : std::cout<<"\\par Description of components\n\n";
369 0 : std::cout<<cstring<<"\n\n";
370 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
371 : printf("<tr> <td width=5%%> <b> Quantity </b> </td> <td> <b> Keyword </b> </td> <td> <b> Description </b> </td> </tr>\n");
372 0 : for(unsigned i=0; i<cnames.size(); ++i) {
373 0 : if( exists(ckey.find(cnames[i])->second) ) {
374 : printf("<tr>\n");
375 : printf("<td width=5%%> <b> %s </b></td> <td width=10%%> <b> %s </b> </td> \n",
376 : cnames[i].c_str(),(ckey.find(cnames[i])->second).c_str() );
377 : printf("<td> %s </td>\n",(cdocs.find(cnames[i])->second).c_str() );
378 : printf("</tr>\n");
379 : }
380 : }
381 0 : std::cout<<"</table>\n\n";
382 : }
383 : }
384 : }
385 :
386 : unsigned nkeys=0;
387 0 : for(unsigned i=0; i<keys.size(); ++i) {
388 0 : if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
389 : }
390 0 : if( nkeys>0 ) {
391 0 : if(isaction && isatoms) std::cout<<"\\par The atoms involved can be specified using\n\n";
392 0 : else if(isaction) std::cout<<"\\par The data to analyze can be the output from another analysis algorithm\n\n";
393 0 : else std::cout<<"\\par The input trajectory is specified using one of the following\n\n";
394 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
395 0 : std::string prevtag="start"; unsigned counter=0;
396 0 : for(unsigned i=0; i<keys.size(); ++i) {
397 0 : if ( (types.find(keys[i])->second).isAtomList() ) {
398 0 : plumed_massert( atomtags.count(keys[i]), "keyword " + keys[i] + " allegedly specifies atoms but no tag has been specified. Please email Gareth Tribello");
399 0 : if( prevtag!="start" && prevtag!=atomtags.find(keys[i])->second && isaction ) {
400 0 : std::cout<<"</table>\n\n";
401 0 : if( isatoms ) std::cout<<"\\par Or alternatively by using\n\n";
402 0 : else if( counter==0 ) { std::cout<<"\\par Alternatively data can be collected from the trajectory using \n\n"; counter++; }
403 0 : else std::cout<<"\\par Lastly data collected in a previous analysis action can be reanalyzed by using the keyword \n\n";
404 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
405 : }
406 0 : print_html_item( keys[i] );
407 0 : prevtag=atomtags.find(keys[i])->second;
408 : }
409 : }
410 0 : std::cout<<"</table>\n\n";
411 : }
412 : nkeys=0;
413 0 : for(unsigned i=0; i<keys.size(); ++i) {
414 0 : if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
415 : }
416 0 : if( nkeys>0 ) {
417 0 : if(isaction) std::cout<< "\\par Compulsory keywords\n\n";
418 0 : else std::cout<<"\\par The following must be present\n\n";
419 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
420 0 : for(unsigned i=0; i<keys.size(); ++i) {
421 0 : if ( (types.find(keys[i])->second).isCompulsory() ) print_html_item( keys[i] );
422 : }
423 0 : std::cout<<"</table>\n\n";
424 : }
425 : nkeys=0;
426 0 : for(unsigned i=0; i<keys.size(); ++i) {
427 0 : if ( (types.find(keys[i])->second).isFlag() || (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) nkeys++;
428 : }
429 0 : if( nkeys>0 ) {
430 0 : if(isaction) std::cout<<"\\par Options\n\n";
431 0 : else std::cout<<"\\par The following options are available\n\n";
432 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
433 0 : for(unsigned i=0; i<keys.size(); ++i) {
434 0 : if ( (types.find(keys[i])->second).isFlag() ) print_html_item( keys[i] );
435 : }
436 0 : std::cout<<"\n";
437 : }
438 : nkeys=0;
439 0 : for(unsigned i=0; i<keys.size(); ++i) {
440 0 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) nkeys++;
441 : }
442 0 : if( nkeys>0 ) {
443 0 : for(unsigned i=0; i<keys.size(); ++i) {
444 0 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) print_html_item( keys[i] );
445 : }
446 : }
447 0 : std::cout<<"</table>\n\n";
448 0 : }
449 :
450 0 : void Keywords::print_spelling() const {
451 0 : for(unsigned i=0; i<keys.size(); ++i) printf("%s\n", keys[i].c_str() );
452 0 : for(unsigned i=0; i<cnames.size(); ++i) printf("%s\n",cnames[i].c_str() );
453 0 : }
454 :
455 270 : void Keywords::print( FILE* out ) const {
456 : unsigned nkeys=0;
457 8186 : for(unsigned i=0; i<keys.size(); ++i) {
458 3823 : if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
459 : }
460 270 : if( nkeys>0 ) {
461 : fprintf(out,"The input trajectory can be in any of the following formats: \n\n");
462 4560 : for(unsigned i=0; i<keys.size(); ++i) {
463 2403 : if ( (types.find(keys[i])->second).isAtomList() ) printKeyword( keys[i], out );
464 : }
465 : }
466 : nkeys=0;
467 7916 : for(unsigned i=0; i<keys.size(); ++i) {
468 3823 : if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
469 : }
470 : unsigned ncompulsory=nkeys;
471 270 : if( nkeys>0 ) {
472 : fprintf(out,"\nThe following arguments are compulsory: \n\n");
473 6578 : for(unsigned i=0; i<keys.size(); ++i) {
474 3861 : if ( (types.find(keys[i])->second).isCompulsory() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
475 : }
476 : }
477 : nkeys=0;
478 7916 : for(unsigned i=0; i<keys.size(); ++i) {
479 3823 : if ( (types.find(keys[i])->second).isFlag() ) nkeys++;
480 : }
481 270 : if( nkeys>0 ) {
482 234 : if(ncompulsory>0) fprintf( out,"\nIn addition you may use the following options: \n\n");
483 : else fprintf( out,"\nThe following options are available\n\n");
484 7512 : for(unsigned i=0; i<keys.size(); ++i) {
485 4491 : if ( (types.find(keys[i])->second).isFlag() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
486 : }
487 : }
488 : nkeys=0;
489 7916 : for(unsigned i=0; i<keys.size(); ++i) {
490 6917 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) nkeys++;
491 : }
492 270 : if( nkeys>0 ) {
493 6852 : for(unsigned i=0; i<keys.size(); ++i) {
494 7168 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
495 : }
496 : fprintf(out,"\n");
497 : }
498 270 : }
499 :
500 3123 : void Keywords::printKeyword( const std::string& key, FILE* out ) const {
501 3123 : bool killdot=( (documentation.find(key)->second).find("\\f$")!=std::string::npos ); // Check for latex
502 3123 : std::vector<std::string> w=Tools::getWords( documentation.find(key)->second );
503 : fprintf(out,"%23s - ", key.c_str() );
504 3123 : unsigned nl=0; std::string blank=" ";
505 132766 : for(unsigned i=0; i<w.size(); ++i) {
506 63544 : nl+=w[i].length() + 1;
507 63544 : if( nl>60 ) {
508 : fprintf(out,"\n%23s %s ", blank.c_str(), w[i].c_str() ); nl=0;
509 : } else {
510 : fprintf(out,"%s ", w[i].c_str() );
511 : }
512 65923 : if( killdot && w[i].find(".")!=std::string::npos ) break; // If there is latex only write up to first dot
513 : }
514 3123 : fprintf(out,"\n");
515 3123 : }
516 :
517 0 : void Keywords::print( Log& log ) const {
518 : unsigned nkeys=0;
519 0 : for(unsigned i=0; i<keys.size(); ++i) {
520 0 : if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
521 : }
522 0 : if (nkeys>0 ) {
523 0 : log.printf( "The input for this keyword can be specified using one of the following \n\n");
524 0 : for(unsigned i=0; i<keys.size(); ++i) {
525 0 : if ( (types.find(keys[i])->second).isAtomList() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
526 : }
527 : }
528 : nkeys=0;
529 0 : for(unsigned i=0; i<keys.size(); ++i) {
530 0 : if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
531 : }
532 0 : if( nkeys>0 ) {
533 0 : log.printf( "\n The compulsory keywords for this action are: \n\n");
534 0 : for(unsigned i=0; i<keys.size(); ++i) {
535 0 : if ( (types.find(keys[i])->second).isCompulsory() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
536 : }
537 : }
538 : nkeys=0;
539 0 : for(unsigned i=0; i<keys.size(); ++i) {
540 0 : if ( (types.find(keys[i])->second).isFlag() ) nkeys++;
541 : }
542 0 : if( nkeys>0 ) {
543 0 : log.printf( "\n The following options are available: \n\n");
544 0 : for(unsigned i=0; i<keys.size(); ++i) {
545 0 : if ( (types.find(keys[i])->second).isFlag() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
546 : }
547 0 : log.printf("\n");
548 : }
549 : nkeys=0;
550 0 : for(unsigned i=0; i<keys.size(); ++i) {
551 0 : if ( (types.find(keys[i])->second).isOptional() ) nkeys++;
552 : }
553 0 : if( nkeys>0 ) {
554 0 : for(unsigned i=0; i<keys.size(); ++i) {
555 0 : if ( (types.find(keys[i])->second).isOptional() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
556 : }
557 0 : log.printf("\n");
558 : }
559 0 : }
560 :
561 0 : void Keywords::printKeyword( const std::string& key, Log& log ) const {
562 0 : bool killdot=( (documentation.find(key)->second).find("\\f$")!=std::string::npos ); // Check for latex
563 0 : std::vector<std::string> w=Tools::getWords( documentation.find(key)->second );
564 0 : log.printf("%23s - ", key.c_str() );
565 0 : unsigned nl=0; std::string blank=" ";
566 0 : for(unsigned i=0; i<w.size(); ++i) {
567 0 : nl+=w[i].length() + 1;
568 0 : if( nl>60 ) {
569 0 : log.printf("\n%23s %s ", blank.c_str(), w[i].c_str() ); nl=0;
570 : } else {
571 0 : log.printf("%s ", w[i].c_str() );
572 : }
573 0 : if( killdot && w[i].find(".")!=std::string::npos ) break; // If there is latex only write up to first dot
574 : }
575 0 : log.printf("\n");
576 0 : }
577 :
578 0 : void Keywords::print_html_item( const std::string& key ) const {
579 : printf("<tr>\n");
580 : printf("<td width=15%%> <b> %s </b></td>\n",key.c_str() );
581 : printf("<td> %s </td>\n",(documentation.find(key)->second).c_str() );
582 : printf("</tr>\n");
583 0 : }
584 :
585 303635 : std::string Keywords::get( const unsigned k ) const {
586 303635 : plumed_assert( k<size() );
587 607270 : return keys[k];
588 : }
589 :
590 13527 : bool Keywords::getLogicalDefault( std::string key, bool& def ) const {
591 13527 : if( booldefs.find(key)!=booldefs.end() ) {
592 13527 : def=booldefs.find(key)->second;
593 13527 : return true;
594 : } else {
595 : return false;
596 : }
597 : }
598 :
599 9195 : bool Keywords::getDefaultValue( std::string key, std::string& def ) const {
600 23082 : plumed_assert( style(key,"compulsory") || style(key,"hidden") );
601 :
602 9195 : if( numdefs.find(key)!=numdefs.end() ) {
603 4503 : def=numdefs.find(key)->second;
604 : return true;
605 : } else {
606 : return false;
607 : }
608 : }
609 :
610 0 : void Keywords::destroyData() {
611 0 : keys.clear(); reserved_keys.clear(); types.clear();
612 : allowmultiple.clear(); documentation.clear();
613 : booldefs.clear(); numdefs.clear(); atomtags.clear();
614 : ckey.clear(); cdocs.clear(); ckey.clear();
615 0 : }
616 :
617 5492 : void Keywords::setComponentsIntroduction( const std::string& instr ) {
618 5492 : cstring = instr;
619 5492 : }
620 :
621 44080 : void Keywords::addOutputComponent( const std::string& name, const std::string& key, const std::string& descr ) {
622 44080 : plumed_assert( !outputComponentExists( name, false ) );
623 44080 : plumed_massert( name.find("-")==std::string::npos,"dash is reseved character in component names" );
624 :
625 44080 : std::size_t num2=name.find_first_of("_");
626 44080 : if( num2!=std::string::npos ) plumed_massert( num2==0, "underscore is reserved character in component names that has special meaning");
627 :
628 88160 : ckey.insert( std::pair<std::string,std::string>(name,key) );
629 88160 : cdocs.insert( std::pair<std::string,std::string>(name,descr) );
630 44080 : cnames.push_back(name);
631 44080 : }
632 :
633 77519 : bool Keywords::outputComponentExists( const std::string& name, const bool& custom ) const {
634 77519 : if( custom && cstring.find("customize")!=std::string::npos ) return true;
635 :
636 : std::string sname;
637 74131 : std::size_t num=name.find_first_of("-");
638 74131 : std::size_t num2=name.find_last_of("_");
639 :
640 76009 : if( num2!=std::string::npos ) sname=name.substr(num2);
641 98156 : else if( num!=std::string::npos ) sname=name.substr(0,num);
642 : else sname=name;
643 :
644 1388804 : for(unsigned i=0; i<cnames.size(); ++i) {
645 650322 : if( sname==cnames[i] ) return true;
646 : }
647 : return false;
648 : }
649 :
650 5874 : }
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