Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2018 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 "ActionWithValue.h"
23 : #include "tools/Exception.h"
24 : #include "tools/OpenMP.h"
25 :
26 : using namespace std;
27 : namespace PLMD {
28 :
29 1594 : void ActionWithValue::registerKeywords(Keywords& keys) {
30 : keys.setComponentsIntroduction("By default the value of the calculated quantity can be referenced elsewhere in the "
31 : "input file by using the label of the action. Alternatively this Action can be used "
32 : "to calculate the following quantities by employing the keywords listed "
33 : "below. These quanties can be referenced elsewhere in the input by using this Action's "
34 1594 : "label followed by a dot and the name of the quantity required from the list below.");
35 1594 : keys.addFlag("NUMERICAL_DERIVATIVES", false, "calculate the derivatives for these quantities numerically");
36 1594 : }
37 :
38 0 : void ActionWithValue::noAnalyticalDerivatives(Keywords& keys) {
39 0 : keys.remove("NUMERICAL_DERIVATIVES");
40 0 : keys.addFlag("NUMERICAL_DERIVATIVES",true,"analytical derivatives are not implemented for this keyword so numerical derivatives are always used");
41 0 : }
42 :
43 353 : void ActionWithValue::componentsAreNotOptional(Keywords& keys) {
44 : keys.setComponentsIntroduction("By default this Action calculates the following quantities. These quanties can "
45 : "be referenced elsewhere in the input by using this Action's label followed by a "
46 353 : "dot and the name of the quantity required from the list below.");
47 353 : }
48 :
49 137 : void ActionWithValue::useCustomisableComponents(Keywords& keys) {
50 : keys.setComponentsIntroduction("The names of the components in this action can be customized by the user in the "
51 : "actions input file. However, in addition to these customizable components the "
52 137 : "following quantities will always be output");
53 137 : }
54 :
55 1473 : ActionWithValue::ActionWithValue(const ActionOptions&ao):
56 : Action(ao),
57 : noderiv(true),
58 1473 : numericalDerivatives(false)
59 : {
60 1473 : if( keywords.exists("NUMERICAL_DERIVATIVES") ) parseFlag("NUMERICAL_DERIVATIVES",numericalDerivatives);
61 1473 : if(numericalDerivatives) log.printf(" using numerical derivatives\n");
62 1473 : }
63 :
64 2946 : ActionWithValue::~ActionWithValue() {
65 1473 : for(unsigned i=0; i<values.size(); ++i)delete values[i];
66 1473 : }
67 :
68 77878 : void ActionWithValue::clearInputForces() {
69 77878 : for(unsigned i=0; i<values.size(); i++) values[i]->clearInputForce();
70 77878 : }
71 :
72 80521 : void ActionWithValue::clearDerivatives() {
73 80521 : unsigned nt = OpenMP::getNumThreads();
74 239822 : #pragma omp parallel num_threads(nt)
75 : {
76 160517 : #pragma omp for
77 318168 : for(unsigned i=0; i<values.size(); i++) values[i]->clearDerivatives();
78 : }
79 80521 : }
80 :
81 : // -- These are the routine for copying the value pointers to other classes -- //
82 :
83 113785 : bool ActionWithValue::exists( const std::string& name ) const {
84 20569371 : for(unsigned i=0; i<values.size(); ++i) {
85 20472454 : if (values[i]->name==name) return true;
86 : }
87 96917 : return false;
88 : }
89 :
90 16880 : Value* ActionWithValue::copyOutput( const std::string& name ) const {
91 7988991 : for(unsigned i=0; i<values.size(); ++i) {
92 7988991 : if (values[i]->name==name) return values[i];
93 : }
94 0 : plumed_merror("there is no pointer with name " + name);
95 : return NULL;
96 : }
97 :
98 7541 : Value* ActionWithValue::copyOutput( const unsigned& n ) const {
99 7541 : plumed_massert(n<values.size(),"you have requested a pointer that is out of bounds");
100 7541 : return values[n];
101 : }
102 :
103 : // -- HERE WE HAVE THE STUFF FOR THE DEFAULT VALUE -- //
104 :
105 17 : void ActionWithValue::addValue() {
106 17 : plumed_massert(values.empty(),"You have already added the default value for this action");
107 17 : values.push_back(new Value(this,getLabel(), false ) );
108 17 : }
109 :
110 722 : void ActionWithValue::addValueWithDerivatives() {
111 722 : plumed_massert(values.empty(),"You have already added the default value for this action");
112 722 : values.push_back(new Value(this,getLabel(), true ) );
113 722 : }
114 :
115 651 : void ActionWithValue::setNotPeriodic() {
116 651 : plumed_massert(values.size()==1,"The number of components is not equal to one");
117 651 : plumed_massert(values[0]->name==getLabel(), "The value you are trying to set is not the default");
118 651 : values[0]->min=0; values[0]->max=0;
119 651 : values[0]->setupPeriodicity();
120 651 : }
121 :
122 88 : void ActionWithValue::setPeriodic( const std::string& min, const std::string& max ) {
123 88 : plumed_massert(values.size()==1,"The number of components is not equal to one");
124 88 : plumed_massert(values[0]->name==getLabel(), "The value you are trying to set is not the default");
125 88 : values[0]->setDomain( min, max );
126 88 : }
127 :
128 14957279 : Value* ActionWithValue::getPntrToValue() {
129 : plumed_dbg_massert(values.size()==1,"The number of components is not equal to one");
130 : plumed_dbg_massert(values[0]->name==getLabel(), "The value you are trying to retrieve is not the default");
131 14957279 : return values[0];
132 : }
133 :
134 : // -- HERE WE HAVE THE STUFF FOR NAMED VALUES / COMPONENTS -- //
135 :
136 3251 : void ActionWithValue::addComponent( const std::string& name ) {
137 3251 : if( !keywords.outputComponentExists(name,true) ) {
138 0 : warning("a description of component " + name + " has not been added to the manual. Components should be registered like keywords in "
139 0 : "registerKeywords as described in the developer docs.");
140 : }
141 3251 : std::string thename; thename=getLabel() + "." + name;
142 2604187 : for(unsigned i=0; i<values.size(); ++i) {
143 2600936 : plumed_massert(values[i]->name!=getLabel(),"Cannot mix single values with components");
144 2600936 : plumed_massert(values[i]->name!=thename&&name!="bias","Since PLUMED 2.3 the component 'bias' is automatically added to all biases by the general constructor!\n"
145 0 : "Remove the line addComponent(\"bias\") from your bias.");
146 2600936 : plumed_massert(values[i]->name!=thename,"there is already a value with this name");
147 : }
148 3251 : values.push_back(new Value(this,thename, false ) );
149 6502 : std::string msg=" added component to this action: "+thename+" \n";
150 6502 : log.printf(msg.c_str());
151 3251 : }
152 :
153 7053 : void ActionWithValue::addComponentWithDerivatives( const std::string& name ) {
154 7053 : if( !keywords.outputComponentExists(name,true) ) {
155 2 : warning("a description of component " + name + " has not been added to the manual. Components should be registered like keywords in "
156 1 : "registerKeywords as described in the developer doc.");
157 : }
158 7053 : std::string thename; thename=getLabel() + "." + name;
159 1740563 : for(unsigned i=0; i<values.size(); ++i) {
160 1733510 : plumed_massert(values[i]->name!=getLabel(),"Cannot mix single values with components");
161 1733510 : plumed_massert(values[i]->name!=thename&&name!="bias","Since PLUMED 2.3 the component 'bias' is automatically added to all biases by the general constructor!\n"
162 0 : "Remove the line addComponentWithDerivatives(\"bias\") from your bias.");
163 1733510 : plumed_massert(values[i]->name!=thename,"there is already a value with this name");
164 : }
165 7053 : values.push_back(new Value(this,thename, true ) );
166 14106 : std::string msg=" added component to this action: "+thename+" \n";
167 14106 : log.printf(msg.c_str());
168 7053 : }
169 :
170 90143 : int ActionWithValue::getComponent( const std::string& name ) const {
171 90143 : plumed_massert( !exists( getLabel() ), "You should not be calling this routine if you are using a value");
172 90143 : std::string thename; thename=getLabel() + "." + name;
173 8290767 : for(unsigned i=0; i<values.size(); ++i) {
174 8290767 : if (values[i]->name==thename) return i;
175 : }
176 0 : plumed_merror("there is no component with name " + name);
177 90143 : return -1;
178 : }
179 :
180 0 : std::string ActionWithValue::getComponentsList( ) const {
181 0 : std::string complist;
182 0 : for(unsigned i=0; i<values.size(); ++i) {
183 0 : complist+=values[i]->name+" ";
184 : }
185 0 : return complist;
186 : }
187 :
188 485 : std::vector<std::string> ActionWithValue::getComponentsVector( ) const {
189 485 : std::vector<std::string> complist;
190 173218 : for(unsigned i=0; i<values.size(); ++i) {
191 172733 : complist.push_back(values[i]->name);
192 : }
193 485 : return complist;
194 : }
195 :
196 7244 : void ActionWithValue::componentIsNotPeriodic( const std::string& name ) {
197 7244 : int kk=getComponent(name);
198 7244 : values[kk]->min=0; values[kk]->max=0;
199 7244 : values[kk]->setupPeriodicity();
200 7244 : }
201 :
202 38 : void ActionWithValue::componentIsPeriodic( const std::string& name, const std::string& min, const std::string& max ) {
203 38 : int kk=getComponent(name);
204 38 : values[kk]->setDomain(min,max);
205 38 : }
206 :
207 77878 : void ActionWithValue::setGradientsIfNeeded() {
208 77878 : if(isOptionOn("GRADIENTS")) {
209 402 : for(unsigned i=0; i<values.size(); i++) values[i]->setGradients();
210 : }
211 77878 : }
212 :
213 3483411 : void ActionWithValue::turnOnDerivatives() {
214 : // Turn on the derivatives
215 3483411 : noderiv=false;
216 : // Resize the derivatives
217 3483411 : for(unsigned i=0; i<values.size(); ++i) values[i]->resizeDerivatives( getNumberOfDerivatives() );
218 : // And turn on the derivatives in all actions on which we are dependent
219 6965796 : for(unsigned i=0; i<getDependencies().size(); ++i) {
220 3482385 : ActionWithValue* vv=dynamic_cast<ActionWithValue*>( getDependencies()[i] );
221 3482385 : if(vv) vv->turnOnDerivatives();
222 : }
223 3483411 : }
224 :
225 82861 : Value* ActionWithValue::getPntrToComponent( const std::string& name ) {
226 82861 : int kk=getComponent(name);
227 82861 : return values[kk];
228 : }
229 :
230 190228 : Value* ActionWithValue::getPntrToComponent( int n ) {
231 : plumed_dbg_massert(n<values.size(),"you have requested a pointer that is out of bounds");
232 190228 : return values[n];
233 : }
234 :
235 2523 : }
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