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 386081 : Keywords::KeyType::KeyType( const std::string& type ) {
30 386081 : if( type=="compulsory" ) {
31 105674 : style=compulsory;
32 280407 : } else if( type=="flag" ) {
33 65553 : style=flag;
34 214854 : } else if( type=="optional" ) {
35 110634 : style=optional;
36 156844 : } else if( type.find("atoms")!=std::string::npos || type.find("residues")!=std::string::npos ) {
37 51640 : style=atoms;
38 52580 : } else if( type=="hidden" ) {
39 25159 : style=hidden;
40 27421 : } else if( type=="vessel" ) {
41 27421 : style=vessel;
42 : } else {
43 0 : plumed_massert(false,"invalid keyword specifier " + type);
44 : }
45 386081 : }
46 :
47 1832 : void Keywords::KeyType::setStyle( const std::string& type ) {
48 1832 : if( type=="compulsory" ) {
49 35 : style=compulsory;
50 1797 : } else if( type=="flag" ) {
51 0 : style=flag;
52 1797 : } else if( type=="optional" ) {
53 7 : style=optional;
54 3403 : } else if( type.find("atoms")!=std::string::npos || type.find("residues")!=std::string::npos ) {
55 177 : style=atoms;
56 1613 : } else if( type=="hidden" ) {
57 0 : style=hidden;
58 1613 : } else if( type=="vessel" ) {
59 1613 : style=vessel;
60 : } else {
61 0 : plumed_massert(false,"invalid keyword specifier " + type);
62 : }
63 1832 : }
64 :
65 513 : void Keywords::add( const Keywords& newkeys ) {
66 513 : newkeys.copyData( keys, reserved_keys, types, allowmultiple, documentation, booldefs, numdefs, atomtags, cnames, ckey, cdocs );
67 513 : }
68 :
69 513 : 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 1026 : for(unsigned i=0; i<keys.size(); ++i) {
74 : 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 28728 : for(unsigned i=0; i<reserved_keys.size(); ++i) {
89 : std::string thiskey=reserved_keys[i];
90 246024 : for(unsigned j=0; j<kk.size(); ++j) plumed_massert( thiskey!=kk[j], "keyword " + thiskey + " is in twice" );
91 370683 : for(unsigned j=0; j<rk.size(); ++j) plumed_massert( thiskey!=rk[j], "keyword " + thiskey + " is in twice" );
92 9234 : rk.push_back( thiskey );
93 0 : plumed_massert( types.count( thiskey ), "no type data on keyword " + thiskey + " to copy" );
94 9234 : tt.insert( std::pair<std::string,KeyType>( thiskey,types.find(thiskey)->second) );
95 9234 : if( (types.find(thiskey)->second).isAtomList() ) atags.insert( std::pair<std::string,std::string>( thiskey,atomtags.find(thiskey)->second) );
96 0 : plumed_massert( allowmultiple.count( thiskey ), "no numbered data on keyword " + thiskey + " to copy" );
97 9234 : am.insert( std::pair<std::string,bool>(thiskey,allowmultiple.find(thiskey)->second) );
98 0 : plumed_massert( documentation.count( thiskey ), "no documentation for keyword " + thiskey + " to copy" );
99 18468 : docs.insert( std::pair<std::string,std::string>(thiskey,documentation.find(thiskey)->second) );
100 0 : if( booldefs.count( thiskey ) ) bools.insert( std::pair<std::string,bool>( thiskey,booldefs.find(thiskey)->second) );
101 0 : if( numdefs.count( thiskey ) ) nums.insert( std::pair<std::string,std::string>( thiskey,numdefs.find(thiskey)->second) );
102 : }
103 28728 : for(unsigned i=0; i<cnames.size(); ++i) {
104 : std::string thisnam=cnames[i];
105 253935 : for(unsigned j=0; j<cnam.size(); ++j) plumed_massert( thisnam!=cnam[j], "component " + thisnam + " is in twice" );
106 9234 : cnam.push_back( thisnam );
107 0 : plumed_massert( ckey.count( thisnam ), "no keyword data on component " + thisnam + " to copy" );
108 18468 : ck.insert( std::pair<std::string,std::string>( thisnam, ckey.find(thisnam)->second) );
109 0 : plumed_massert( cdocs.count( thisnam ), "no documentation on component " + thisnam + " to copy" );
110 18468 : cd.insert( std::pair<std::string,std::string>( thisnam, cdocs.find(thisnam)->second) );
111 : }
112 513 : }
113 :
114 51266 : void Keywords::reserve( const std::string & t, const std::string & k, const std::string & d ) {
115 51266 : plumed_assert( !exists(k) && !reserved(k) );
116 : std::string fd, lowkey=k;
117 : // Convert to lower case
118 51266 : std::transform(lowkey.begin(),lowkey.end(),lowkey.begin(),tolower);
119 : // Remove any underscore characters
120 : for(unsigned i=0;; ++i) {
121 : std::size_t num=lowkey.find_first_of("_");
122 69555 : if( num==std::string::npos ) break;
123 18289 : lowkey.erase( lowkey.begin() + num, lowkey.begin() + num + 1 );
124 18289 : }
125 51266 : if( t=="vessel" ) {
126 82263 : fd = d + " The final value can be referenced using <em>label</em>." + lowkey;
127 51616 : if(d.find("flag")==std::string::npos) fd += ". You can use multiple instances of this keyword i.e. " +
128 145170 : k +"1, " + k + "2, " + k + "3... The corresponding values are then "
129 120975 : "referenced using <em>label</em>."+ lowkey +"-1, <em>label</em>." + lowkey +
130 72585 : "-2, <em>label</em>." + lowkey + "-3...";
131 27421 : allowmultiple.insert( std::pair<std::string,bool>(k,true) );
132 82263 : types.insert( std::pair<std::string,KeyType>(k,KeyType("vessel")) );
133 23845 : } else if( t=="numbered" ) {
134 16760 : fd = d + " You can use multiple instances of this keyword i.e. " + k +"1, " + k + "2, " + k + "3...";
135 2095 : allowmultiple.insert( std::pair<std::string,bool>(k,true) );
136 6285 : types.insert( std::pair<std::string,KeyType>(k,KeyType("optional")) );
137 : } else {
138 : fd = d;
139 21750 : if( t=="atoms" && isaction ) fd = d + ". For more information on how to specify lists of atoms see \\ref Group";
140 21750 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
141 43500 : types.insert( std::pair<std::string,KeyType>(k,KeyType(t)) );
142 22947 : if( (types.find(k)->second).isAtomList() ) atomtags.insert( std::pair<std::string,std::string>(k,t) );
143 : }
144 102532 : documentation.insert( std::pair<std::string,std::string>(k,fd) );
145 51266 : reserved_keys.push_back(k);
146 51266 : }
147 :
148 1602 : void Keywords::reserveFlag( const std::string & k, const bool def, const std::string & d ) {
149 1602 : plumed_assert( !exists(k) && !reserved(k) );
150 : std::string defstr;
151 1602 : if( def ) { defstr="( default=on ) "; } else { defstr="( default=off ) "; }
152 4806 : types.insert( std::pair<std::string,KeyType>(k,KeyType("flag")) );
153 1602 : std::string fd,lowkey=k; std::transform(lowkey.begin(),lowkey.end(),lowkey.begin(),tolower);
154 3204 : fd=defstr + d;
155 3204 : documentation.insert( std::pair<std::string,std::string>(k,fd) );
156 1602 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
157 1602 : booldefs.insert( std::pair<std::string,bool>(k,def) );
158 1602 : reserved_keys.push_back(k);
159 1602 : }
160 :
161 11547 : void Keywords::use( const std::string & k ) {
162 11547 : plumed_massert( reserved(k), "the " + k + " keyword is not reserved");
163 452634 : for(unsigned i=0; i<reserved_keys.size(); ++i) {
164 143180 : if(reserved_keys[i]==k) keys.push_back( reserved_keys[i] );
165 : }
166 11547 : }
167 :
168 1832 : void Keywords::reset_style( const std::string & k, const std::string & style ) {
169 1832 : plumed_assert( exists(k) || reserved(k) );
170 1832 : (types.find(k)->second).setStyle(style);
171 3445 : if( (types.find(k)->second).isVessel() ) allowmultiple[k]=true;
172 2009 : if( (types.find(k)->second).isAtomList() ) atomtags.insert( std::pair<std::string,std::string>(k,style) );
173 1832 : }
174 :
175 186986 : void Keywords::add( const std::string & t, const std::string & k, const std::string & d ) {
176 560958 : plumed_massert( !exists(k) && t!="flag" && !reserved(k) && t!="vessel", "keyword " + k + " has already been registered");
177 : std::string fd;
178 186986 : if( t=="numbered" ) {
179 8568 : fd=d + " You can use multiple instances of this keyword i.e. " + k +"1, " + k + "2, " + k + "3...";
180 1071 : allowmultiple.insert( std::pair<std::string,bool>(k,true) );
181 3213 : types.insert( std::pair<std::string,KeyType>(k, KeyType("optional")) );
182 : } else {
183 : fd=d;
184 185915 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
185 371830 : types.insert( std::pair<std::string,KeyType>(k,KeyType(t)) );
186 236358 : if( (types.find(k)->second).isAtomList() ) atomtags.insert( std::pair<std::string,std::string>(k,t) );
187 : }
188 191767 : if( t=="atoms" && isaction ) fd = d + ". For more information on how to specify lists of atoms see \\ref Group";
189 373972 : documentation.insert( std::pair<std::string,std::string>(k,fd) );
190 186986 : keys.push_back(k);
191 186986 : }
192 :
193 82276 : void Keywords::add( const std::string & t, const std::string & k, const std::string & def, const std::string & d ) {
194 164552 : plumed_assert( !exists(k) && !reserved(k) && (t=="compulsory" || t=="hidden" )); // An optional keyword can't have a default
195 164552 : types.insert( std::pair<std::string,KeyType>(k, KeyType(t)) );
196 411380 : documentation.insert( std::pair<std::string,std::string>(k,"( default=" + def + " ) " + d) );
197 82276 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
198 164552 : numdefs.insert( std::pair<std::string,std::string>(k,def) );
199 82276 : keys.push_back(k);
200 82276 : }
201 :
202 63951 : void Keywords::addFlag( const std::string & k, const bool def, const std::string & d ) {
203 63951 : plumed_massert( !exists(k) && !reserved(k), "keyword " + k + " has already been registered");
204 : std::string defstr;
205 63951 : if( def ) { defstr="( default=on ) "; } else { defstr="( default=off ) "; }
206 191853 : types.insert( std::pair<std::string,KeyType>(k,KeyType("flag")) );
207 191853 : documentation.insert( std::pair<std::string,std::string>(k,defstr + d) );
208 63951 : allowmultiple.insert( std::pair<std::string,bool>(k,false) );
209 63951 : booldefs.insert( std::pair<std::string,bool>(k,def) );
210 63951 : keys.push_back(k);
211 63951 : }
212 :
213 881 : void Keywords::remove( const std::string & k ) {
214 : bool found=false; unsigned j=0, n=0;
215 :
216 : while(true) {
217 25014 : for(j=0; j<keys.size(); j++) if(keys[j]==k)break;
218 49740 : for(n=0; n<reserved_keys.size(); n++) if(reserved_keys[n]==k)break;
219 1762 : if(j<keys.size()) {
220 877 : keys.erase(keys.begin()+j);
221 : found=true;
222 885 : } else if(n<reserved_keys.size()) {
223 4 : 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);
229 881 : 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
230 881 : }
231 :
232 6313 : bool Keywords::numbered( const std::string & k ) const {
233 12626 : if( style( k,"atoms") ) return true;
234 0 : plumed_massert( allowmultiple.count(k), "Did not find keyword " + k );
235 4718 : return allowmultiple.find(k)->second;
236 : }
237 :
238 406814 : bool Keywords::style( const std::string & k, const std::string & t ) const {
239 0 : plumed_massert( types.count(k), "Did not find keyword " + k );
240 :
241 813628 : if( (types.find(k)->second).toString()==t ) return true;
242 322490 : return false;
243 : }
244 :
245 522611 : unsigned Keywords::size() const {
246 522611 : return keys.size();
247 : }
248 :
249 8229 : std::string Keywords::getKeyword( const unsigned i ) const {
250 8229 : plumed_assert( i<size() );
251 16458 : return keys[i];
252 : }
253 :
254 509669 : bool Keywords::exists( const std::string & k ) const {
255 16016545 : for(unsigned i=0; i<keys.size(); ++i) {
256 5103926 : if( keys[i]==k ) return true;
257 : }
258 : return false;
259 : }
260 :
261 399362 : bool Keywords::reserved( const std::string & k ) const {
262 2802943 : for(unsigned i=0; i<reserved_keys.size(); ++i) {
263 681354 : 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 :
309 223 : void Keywords::print_vim() const {
310 9920 : for(unsigned i=0; i<keys.size(); ++i) {
311 3158 : if( (types.find(keys[i])->second).isFlag() ) {
312 : printf( ",flag:%s", keys[i].c_str() );
313 : } else {
314 2441 : if( allowmultiple.find(keys[i])->second ) printf(",numbered:%s",keys[i].c_str() );
315 : else printf(",option:%s",keys[i].c_str() );
316 : }
317 : }
318 223 : fprintf(stdout,"\n");
319 223 : print(stdout);
320 223 : }
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 : 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) std::cout<<"\\par The atoms involved can be specified using\n\n";
392 0 : else std::cout<<"\\par The input trajectory is specified using one of the following\n\n";
393 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
394 0 : std::string prevtag="start";
395 0 : for(unsigned i=0; i<keys.size(); ++i) {
396 0 : if ( (types.find(keys[i])->second).isAtomList() ) {
397 0 : plumed_massert( atomtags.count(keys[i]), "keyword " + keys[i] + " allegedly specifies atoms but no tag has been specified. Please email Gareth Tribello");
398 0 : if( prevtag!="start" && prevtag!=atomtags.find(keys[i])->second && isaction ) {
399 0 : std::cout<<"</table>\n\n";
400 0 : std::cout<<"\\par Or alternatively by using\n\n";
401 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
402 : }
403 0 : print_html_item( keys[i] );
404 0 : prevtag=atomtags.find(keys[i])->second;
405 : }
406 : }
407 0 : std::cout<<"</table>\n\n";
408 : }
409 : nkeys=0;
410 0 : for(unsigned i=0; i<keys.size(); ++i) {
411 0 : if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
412 : }
413 0 : if( nkeys>0 ) {
414 0 : if(isaction) std::cout<< "\\par Compulsory keywords\n\n";
415 0 : else std::cout<<"\\par The following must be present\n\n";
416 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
417 0 : for(unsigned i=0; i<keys.size(); ++i) {
418 0 : if ( (types.find(keys[i])->second).isCompulsory() ) print_html_item( keys[i] );
419 : }
420 0 : std::cout<<"</table>\n\n";
421 : }
422 : nkeys=0;
423 0 : for(unsigned i=0; i<keys.size(); ++i) {
424 0 : if ( (types.find(keys[i])->second).isFlag() || (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) nkeys++;
425 : }
426 0 : if( nkeys>0 ) {
427 0 : if(isaction) std::cout<<"\\par Options\n\n";
428 0 : else std::cout<<"\\par The following options are available\n\n";
429 0 : std::cout<<" <table align=center frame=void width=95%% cellpadding=5%%> \n";
430 0 : for(unsigned i=0; i<keys.size(); ++i) {
431 0 : if ( (types.find(keys[i])->second).isFlag() ) print_html_item( keys[i] );
432 : }
433 0 : std::cout<<"\n";
434 : }
435 : nkeys=0;
436 0 : for(unsigned i=0; i<keys.size(); ++i) {
437 0 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) nkeys++;
438 : }
439 0 : if( nkeys>0 ) {
440 0 : for(unsigned i=0; i<keys.size(); ++i) {
441 0 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) print_html_item( keys[i] );
442 : }
443 0 : std::cout<<"\n";
444 : }
445 0 : std::cout<<"</table>\n\n";
446 0 : }
447 :
448 223 : void Keywords::print( FILE* out ) const {
449 : unsigned nkeys=0;
450 9920 : for(unsigned i=0; i<keys.size(); ++i) {
451 3158 : if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
452 : }
453 223 : if( nkeys>0 ) {
454 : fprintf(out,"The input trajectory can be in any of the following formats: \n\n");
455 5617 : for(unsigned i=0; i<keys.size(); ++i) {
456 2013 : if ( (types.find(keys[i])->second).isAtomList() ) printKeyword( keys[i], out );
457 : }
458 : }
459 : nkeys=0;
460 9920 : for(unsigned i=0; i<keys.size(); ++i) {
461 3158 : if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
462 : }
463 : unsigned ncompulsory=nkeys;
464 223 : if( nkeys>0 ) {
465 : fprintf(out,"\nThe following arguments are compulsory: \n\n");
466 7694 : for(unsigned i=0; i<keys.size(); ++i) {
467 3079 : if ( (types.find(keys[i])->second).isCompulsory() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
468 : }
469 : }
470 : nkeys=0;
471 9920 : for(unsigned i=0; i<keys.size(); ++i) {
472 3158 : if ( (types.find(keys[i])->second).isFlag() ) nkeys++;
473 : }
474 223 : if( nkeys>0 ) {
475 192 : if(ncompulsory>0) fprintf( out,"\nIn addition you may use the following options: \n\n");
476 : else fprintf( out,"\nThe following options are available\n\n");
477 9450 : for(unsigned i=0; i<keys.size(); ++i) {
478 3739 : if ( (types.find(keys[i])->second).isFlag() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
479 : }
480 : }
481 : nkeys=0;
482 9920 : for(unsigned i=0; i<keys.size(); ++i) {
483 5714 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) nkeys++;
484 : }
485 223 : if( nkeys>0 ) {
486 8715 : for(unsigned i=0; i<keys.size(); ++i) {
487 6080 : if ( (types.find(keys[i])->second).isOptional() || (types.find(keys[i])->second).isVessel() ) printKeyword( keys[i], out ); //log.printKeyword( keys[i], documentation[i] );
488 : }
489 : fprintf(out,"\n");
490 : }
491 223 : }
492 :
493 2638 : void Keywords::printKeyword( const std::string& key, FILE* out ) const {
494 2638 : bool killdot=( (documentation.find(key)->second).find("\\f$")!=std::string::npos ); // Check for latex
495 5276 : std::vector<std::string> w=Tools::getWords( documentation.find(key)->second );
496 : fprintf(out,"%23s - ", key.c_str() );
497 2638 : unsigned nl=0; std::string blank=" ";
498 169613 : for(unsigned i=0; i<w.size(); ++i) {
499 55035 : nl+=w[i].length() + 1;
500 55035 : if( nl>60 ) {
501 : fprintf(out,"\n%23s %s ", blank.c_str(), w[i].c_str() ); nl=0;
502 : } else {
503 : fprintf(out,"%s ", w[i].c_str() );
504 : }
505 57092 : if( killdot && w[i].find(".")!=std::string::npos ) break; // If there is latex only write up to first dot
506 : }
507 : fprintf(out,"\n");
508 2638 : }
509 :
510 0 : void Keywords::print( Log& log ) const {
511 : unsigned nkeys=0;
512 0 : for(unsigned i=0; i<keys.size(); ++i) {
513 0 : if ( (types.find(keys[i])->second).isAtomList() ) nkeys++;
514 : }
515 0 : if (nkeys>0 ) {
516 0 : log.printf( "The input for this keyword can be specified using one of the following \n\n");
517 0 : for(unsigned i=0; i<keys.size(); ++i) {
518 0 : if ( (types.find(keys[i])->second).isAtomList() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
519 : }
520 : }
521 : nkeys=0;
522 0 : for(unsigned i=0; i<keys.size(); ++i) {
523 0 : if ( (types.find(keys[i])->second).isCompulsory() ) nkeys++;
524 : }
525 0 : if( nkeys>0 ) {
526 0 : log.printf( "\n The compulsory keywords for this action are: \n\n");
527 0 : for(unsigned i=0; i<keys.size(); ++i) {
528 0 : if ( (types.find(keys[i])->second).isCompulsory() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
529 : }
530 : }
531 : nkeys=0;
532 0 : for(unsigned i=0; i<keys.size(); ++i) {
533 0 : if ( (types.find(keys[i])->second).isFlag() ) nkeys++;
534 : }
535 0 : if( nkeys>0 ) {
536 0 : log.printf( "\n The following options are available: \n\n");
537 0 : for(unsigned i=0; i<keys.size(); ++i) {
538 0 : if ( (types.find(keys[i])->second).isFlag() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
539 : }
540 0 : log.printf("\n");
541 : }
542 : nkeys=0;
543 0 : for(unsigned i=0; i<keys.size(); ++i) {
544 0 : if ( (types.find(keys[i])->second).isOptional() ) nkeys++;
545 : }
546 0 : if( nkeys>0 ) {
547 0 : for(unsigned i=0; i<keys.size(); ++i) {
548 0 : if ( (types.find(keys[i])->second).isOptional() ) printKeyword( keys[i], log ); //log.printKeyword( keys[i], documentation[i] );
549 : }
550 0 : log.printf("\n");
551 : }
552 0 : }
553 :
554 0 : void Keywords::printKeyword( const std::string& key, Log& log ) const {
555 0 : bool killdot=( (documentation.find(key)->second).find("\\f$")!=std::string::npos ); // Check for latex
556 0 : std::vector<std::string> w=Tools::getWords( documentation.find(key)->second );
557 0 : log.printf("%23s - ", key.c_str() );
558 0 : unsigned nl=0; std::string blank=" ";
559 0 : for(unsigned i=0; i<w.size(); ++i) {
560 0 : nl+=w[i].length() + 1;
561 0 : if( nl>60 ) {
562 0 : log.printf("\n%23s %s ", blank.c_str(), w[i].c_str() ); nl=0;
563 : } else {
564 0 : log.printf("%s ", w[i].c_str() );
565 : }
566 0 : if( killdot && w[i].find(".")!=std::string::npos ) break; // If there is latex only write up to first dot
567 : }
568 0 : log.printf("\n");
569 0 : }
570 :
571 0 : void Keywords::print_html_item( const std::string& key ) const {
572 : printf("<tr>\n");
573 : printf("<td width=15%%> <b> %s </b></td>\n",key.c_str() );
574 : printf("<td> %s </td>\n",(documentation.find(key)->second).c_str() );
575 : printf("</tr>\n");
576 0 : }
577 :
578 245442 : std::string Keywords::get( const unsigned k ) const {
579 245442 : plumed_assert( k<size() );
580 490884 : return keys[k];
581 : }
582 :
583 10826 : bool Keywords::getLogicalDefault( std::string key, bool& def ) const {
584 10826 : if( booldefs.find(key)!=booldefs.end() ) {
585 10826 : def=booldefs.find(key)->second;
586 10826 : return true;
587 : } else {
588 : return false;
589 : }
590 : }
591 :
592 7415 : bool Keywords::getDefaultValue( std::string key, std::string& def ) const {
593 22245 : plumed_assert( style(key,"compulsory") || style(key,"hidden") );
594 :
595 7415 : if( numdefs.find(key)!=numdefs.end() ) {
596 3484 : def=numdefs.find(key)->second;
597 : return true;
598 : } else {
599 : return false;
600 : }
601 : }
602 :
603 5792 : void Keywords::destroyData() {
604 5792 : keys.clear(); reserved_keys.clear(); types.clear();
605 : allowmultiple.clear(); documentation.clear();
606 : booldefs.clear(); numdefs.clear(); atomtags.clear();
607 : ckey.clear(); cdocs.clear(); ckey.clear();
608 5792 : }
609 :
610 4918 : void Keywords::setComponentsIntroduction( const std::string& instr ) {
611 4918 : cstring = instr;
612 4918 : }
613 :
614 36077 : void Keywords::addOutputComponent( const std::string& name, const std::string& key, const std::string& descr ) {
615 36077 : plumed_assert( !outputComponentExists( name, false ) );
616 36077 : plumed_massert( name.find("-")==std::string::npos,"dash is reseved character in component names" );
617 :
618 : std::size_t num2=name.find_first_of("_");
619 36077 : if( num2!=std::string::npos ) plumed_massert( num2==0, "underscore is reserved character in component names that has special meaning");
620 :
621 72154 : ckey.insert( std::pair<std::string,std::string>(name,key) );
622 72154 : cdocs.insert( std::pair<std::string,std::string>(name,descr) );
623 36077 : cnames.push_back(name);
624 36077 : }
625 :
626 68839 : bool Keywords::outputComponentExists( const std::string& name, const bool& custom ) const {
627 101298 : if( custom && cstring.find("customizable")!=std::string::npos ) return true;
628 :
629 : std::string sname; std::size_t num=name.find_first_of("-");
630 39667 : if( num!=std::string::npos ) sname=name.substr(0,num);
631 : else {
632 : std::size_t num2=name.find_first_of("_");
633 41277 : if( num2!=std::string::npos ) sname=name.substr(num2);
634 : else sname=name;
635 : }
636 :
637 921433 : for(unsigned i=0; i<cnames.size(); ++i) {
638 284124 : if( sname==cnames[i] ) return true;
639 : }
640 : return false;
641 : }
642 :
643 4839 : }
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