Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2020 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 : #ifndef __PLUMED_tools_Tools_h
23 : #define __PLUMED_tools_Tools_h
24 :
25 : #include "AtomNumber.h"
26 : #include <vector>
27 : #include <string>
28 : #include <cstdio>
29 : #include <cmath>
30 : #include <limits>
31 : #include <algorithm>
32 : #include <sstream>
33 : #include <memory>
34 :
35 : namespace PLMD {
36 :
37 : class IFile;
38 :
39 : /// \ingroup TOOLBOX
40 : /// Very small non-zero number
41 : const double epsilon(std::numeric_limits<double>::epsilon());
42 :
43 : /// \ingroup TOOLBOX
44 : /// Boltzman constant in kj/K
45 : const double kBoltzmann(0.0083144621);
46 :
47 : /// \ingroup TOOLBOX
48 : /// PI
49 : const double pi(3.141592653589793238462643383279502884197169399375105820974944592307);
50 :
51 : /// \ingroup TOOLBOX
52 : /// Empty class which just contains several (static) tools
53 : class Tools {
54 : /// class to convert a string to a generic type T
55 : template<class T>
56 : static bool convertToAny(const std::string & str,T &t);
57 : /// class to convert a string to a real type T.
58 : /// T should be either float, double, or long double
59 : template<class T>
60 : static bool convertToReal(const std::string & str,T &t);
61 : public:
62 : /// Split the line in words using separators.
63 : /// It also take into account parenthesis. Outer parenthesis found are removed from
64 : /// output, and the text between them is considered as a single word. Only the
65 : /// outer parenthesis are processed, to allow nesting them.
66 : /// parlevel, if not NULL, is increased or decreased according to the number of opened/closed parenthesis
67 : static std::vector<std::string> getWords(const std::string & line,const char* sep=NULL,int* parlevel=NULL,const char* parenthesis="{");
68 : /// Get a line from the file pointer ifile
69 : static bool getline(FILE*,std::string & line);
70 : /// Get a parsed line from the file pointer ifile
71 : /// This function already takes care of joining continued lines and splitting the
72 : /// resulting line into an array of words
73 : static bool getParsedLine(IFile&ifile,std::vector<std::string> & line);
74 : /// Convert a string to a double, reading it
75 : static bool convert(const std::string & str,double & t);
76 : /// Convert a string to a long double, reading it
77 : static bool convert(const std::string & str,long double & t);
78 : /// Convert a string to a float, reading it
79 : static bool convert(const std::string & str,float & t);
80 : /// Convert a string to a int, reading it
81 : static bool convert(const std::string & str,int & t);
82 : /// Convert a string to a long int, reading it
83 : static bool convert(const std::string & str,long int & t);
84 : /// Convert a string to an unsigned int, reading it
85 : static bool convert(const std::string & str,unsigned & t);
86 : /// Convert a string to a atom number, reading it
87 : static bool convert(const std::string & str,AtomNumber & t);
88 : /// Convert a string to a string (i.e. copy)
89 : static bool convert(const std::string & str,std::string & t);
90 : /// Convert anything into a string
91 : template<typename T>
92 : static void convert(T i,std::string & str);
93 : /// Remove trailing blanks
94 : static void trim(std::string & s);
95 : /// Remove trailing comments
96 : static void trimComments(std::string & s);
97 : /// Apply pbc for a unitary cell
98 : static double pbc(double);
99 : /// Retrieve a key from a vector of options.
100 : /// It finds a key starting with "key=" or equal to "key" and copy the
101 : /// part after the = on s. E.g.:
102 : /// line.push_back("aa=xx");
103 : /// getKey(line,"aa",s);
104 : /// will set s="xx"
105 : static bool getKey(std::vector<std::string>& line,const std::string & key,std::string & s,int rep=-1);
106 : /// Find a keyword on the input line, eventually deleting it, and saving its value to val
107 : template <class T>
108 : static bool parse(std::vector<std::string>&line,const std::string&key,T&val,int rep=-1);
109 : /// Find a keyword on the input line, eventually deleting it, and saving its value to a vector
110 : template <class T>
111 : static bool parseVector(std::vector<std::string>&line,const std::string&key,std::vector<T>&val,int rep=-1);
112 : /// Find a keyword without arguments on the input line
113 : static bool parseFlag(std::vector<std::string>&line,const std::string&key,bool&val);
114 : /// Find a keyword on the input line, just reporting if it exists or not
115 : static bool findKeyword(const std::vector<std::string>&line,const std::string&key);
116 : /// Interpret atom ranges
117 : static void interpretRanges(std::vector<std::string>&);
118 : /// Remove duplicates from a vector of type T
119 : template <typename T>
120 : static void removeDuplicates(std::vector<T>& vec);
121 : /// interpret ":" syntax for labels
122 : static void interpretLabel(std::vector<std::string>&s);
123 : /// list files in a directory
124 : static std::vector<std::string> ls(const std::string&);
125 : /// removes leading and trailing blanks from a string
126 : static void stripLeadingAndTrailingBlanks( std::string& str );
127 : /// Extract the extensions from a file name.
128 : /// E.g.: extension("pippo.xyz")="xyz".
129 : /// It only returns extensions with a length between 1 and 4
130 : /// E.g.: extension("pippo.12345")="" whereas extenion("pippo.1234")="1234";
131 : /// It is also smart enough to detect "/", so that
132 : /// extension("pippo/.t")="" whereas extension("pippo/a.t")="t"
133 : static std::string extension(const std::string&);
134 : /// Fast int power
135 : static double fastpow(double base,int exp);
136 : /// Modified 0th-order Bessel function of the first kind
137 : static double bessel0(const double& val);
138 : /// Check if a string full starts with string start.
139 : /// Same as full.find(start)==0
140 : static bool startWith(const std::string & full,const std::string &start);
141 : /**
142 : Tool to create a vector of raw pointers from a vector of unique_pointers (const version).
143 : Returning a vector is fast in C++11. It can be used in order to feed a vector<unique_ptr<T>>
144 : to a function that takes a vector<T*>.
145 : \verbatim
146 : // some function that takes a vec
147 : void func(std::vector<Data*> & vec);
148 : std::vector<std::unique_ptr<Data>> vec;
149 : // func(vec); // does not compile
150 : func(Tools::unique2raw(vec)); // compiles
151 : \endverbatim
152 : Notice that the conversion is fast but takes
153 : some time to allocate the new vector and copy the pointers. In case the function
154 : acting on the vector<T*> is very fast and we do not want to add significant overhead,
155 : it might be convenient to store a separate set of raw pointers.
156 : \verbatim
157 : // some function that takes a vec
158 : void func(std::vector<Data*> & vec);
159 : std::vector<std::unique_ptr<Data>> vec;
160 :
161 : // conversion done only once:
162 : auto vec_ptr=Tools::unique2raw(vec);
163 :
164 : for(int i=0;i<1000;i++){
165 : func(vec_ptr);
166 : }
167 : \endverbatim
168 : */
169 : template <typename T>
170 : static std::vector<T*> unique2raw(const std::vector<std::unique_ptr<T>>&);
171 : /// Tool to create a vector of raw pointers from a vector of unique_pointers.
172 : /// See the non const version.
173 : template <typename T>
174 : static std::vector<const T*> unique2raw(const std::vector<std::unique_ptr<const T>>&);
175 : /// Tiny class that changes directory and comes back when going out of scope.
176 : /// In case system calls to change dir are not available it throws an exception.
177 : /// \warning By construction, changing directory breaks thread safety! Use with care.
178 : class DirectoryChanger {
179 : static const size_t buffersize=4096;
180 : char cwd[buffersize]= {0};
181 : public:
182 : explicit DirectoryChanger(const char*path);
183 : ~DirectoryChanger();
184 : };
185 : };
186 :
187 : template <class T>
188 42017 : bool Tools::parse(std::vector<std::string>&line,const std::string&key,T&val,int rep) {
189 : std::string s;
190 84034 : if(!getKey(line,key+"=",s,rep)) return false;
191 18076 : if(s.length()>0 && !convert(s,val))return false;
192 : return true;
193 : }
194 :
195 : template <class T>
196 18301 : bool Tools::parseVector(std::vector<std::string>&line,const std::string&key,std::vector<T>&val,int rep) {
197 : std::string s;
198 36602 : if(!getKey(line,key+"=",s,rep)) return false;
199 8154 : val.clear();
200 21110 : std::vector<std::string> words=getWords(s,"\t\n ,");
201 83297 : for(unsigned i=0; i<words.size(); ++i) {
202 : T v;
203 : std::string s=words[i];
204 20729 : const std::string multi("@replicas:");
205 20729 : if(rep>=0 && startWith(s,multi)) {
206 12 : s=s.substr(multi.length(),s.length());
207 12 : std::vector<std::string> words=getWords(s,"\t\n ,");
208 6 : plumed_assert(rep<static_cast<int>(words.size()));
209 6 : s=words[rep];
210 : }
211 20729 : if(!convert(s,v))return false;
212 20729 : val.push_back(v);
213 : }
214 : return true;
215 : }
216 :
217 : template<typename T>
218 172 : void Tools::removeDuplicates(std::vector<T>& vec)
219 : {
220 : std::sort(vec.begin(), vec.end());
221 : vec.erase(std::unique(vec.begin(), vec.end()), vec.end());
222 172 : }
223 :
224 : inline
225 19098 : bool Tools::parseFlag(std::vector<std::string>&line,const std::string&key,bool&val) {
226 76277 : for(auto p=line.begin(); p!=line.end(); ++p) {
227 58388 : if(key==*p) {
228 1209 : val=true;
229 : line.erase(p);
230 : return true;
231 : }
232 : }
233 : return false;
234 : }
235 :
236 : /// beware: this brings any number into a pbc that ranges from -0.5 to 0.5
237 : inline
238 : double Tools::pbc(double x) {
239 : #ifdef __PLUMED_PBC_WHILE
240 : while (x>0.5) x-=1.0;
241 : while (x<-0.5) x+=1.0;
242 : return x;
243 : #else
244 : if(std::numeric_limits<int>::round_style == std::round_toward_zero) {
245 : const double offset=100.0;
246 1808821958 : const double y=x+offset;
247 1808821958 : if(y>=0) return y-int(y+0.5);
248 4577 : else return y-int(y-0.5);
249 : } else if(std::numeric_limits<int>::round_style == std::round_to_nearest) {
250 : return x-int(x);
251 : } else return x-floor(x+0.5);
252 : #endif
253 : }
254 :
255 : template<typename T>
256 285501 : void Tools::convert(T i,std::string & str) {
257 571002 : std::ostringstream ostr;
258 191195 : ostr<<i;
259 571002 : str=ostr.str();
260 285501 : }
261 :
262 : inline
263 : double Tools::fastpow(double base, int exp)
264 : {
265 80001031 : if(exp<0) {
266 0 : exp=-exp;
267 0 : base=1.0/base;
268 : }
269 : double result = 1.0;
270 276034397 : while (exp)
271 : {
272 196033364 : if (exp & 1)
273 148360079 : result *= base;
274 196033364 : exp >>= 1;
275 196033364 : base *= base;
276 : }
277 :
278 : return result;
279 : }
280 :
281 : template<typename T>
282 13702163 : std::vector<T*> Tools::unique2raw(const std::vector<std::unique_ptr<T>> & x) {
283 13702163 : std::vector<T*> v(x.size());
284 144453310 : for(unsigned i=0; i<x.size(); i++) v[i]=x[i].get();
285 13702163 : return v;
286 : }
287 :
288 : template<typename T>
289 : std::vector<const T*> Tools::unique2raw(const std::vector<std::unique_ptr<const T>> & x) {
290 : std::vector<const T*> v(x.size());
291 : for(unsigned i=0; i<x.size(); i++) v[i]=x[i].get();
292 : return v;
293 : }
294 :
295 : }
296 :
297 : #endif
298 :
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