Can now highlight cpp files that are loaded with LOAD whose contents …

…appear in modals

PlumedToHTML/PlumedFormatter.py

@@ -1,5 +1,8 @@
+from pygments import highlight
 from pygments.formatter import Formatter
 from pygments.token import Text, Comment, Literal, Keyword, Name, Generic, String
+from pygments.lexers.c_cpp import CppLexer
+from pygments.formatters import HtmlFormatter
 from requests.exceptions import InvalidJSONError
 import html
 import json
@@ -141,6 +144,8 @@ def format(self, tokensource, outfile):
                         iff = open( inp, 'r' )
                         fcontent = iff.read()
                         iff.close()
+                        # This does syntax highlighting on cpp files 
+                        if inp.split(".")[-1]=="cpp" : fcontent = highlight( fcontent, CppLexer(), HtmlFormatter() )
                         nfiles = nfiles + 1
                         if len(self.auxinputlines)>0 : 
                            shortversion, allines = "", fcontent.splitlines()

setup.py

@@ -6,7 +6,7 @@
 
 setuptools.setup(
      name='PlumedToHTML',  
-     version='0.98',
+     version='0.99',
      author="Gareth Tribello",
      author_email="[email protected]",
      description="A package for creating pretified HTML for PLUMED files",

tdata/Distance2.cpp

@@ -0,0 +1,131 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   Copyright (c) 2013 The plumed team
+   (see the PEOPLE file at the root of the distribution for a list of names)
+
+   See http://www.plumed-code.org for more information.
+
+   This file is part of plumed, version 2.0.
+
+   plumed is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation, either version 3 of the License, or
+   (at your option) any later version.
+
+   plumed is distributed in the hope that it will be useful,
+   but WITHOUT ANY WARRANTY; without even the implied warranty of
+   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+   GNU Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
+#include "colvar/Colvar.h"
+#include "core/ActionRegister.h"
+
+#include <string>
+#include <cmath>
+
+using namespace std;
+
+namespace PLMD{
+
+class Distance : public colvar::Colvar {
+  bool components;
+  bool pbc;
+
+public:
+  static void registerKeywords( Keywords& keys );
+  Distance(const ActionOptions&);
+// active methods:
+  virtual void calculate();
+};
+
+PLUMED_REGISTER_ACTION(Distance,"DISTANCE2")
+
+void Distance::registerKeywords( Keywords& keys ){
+  Colvar::registerKeywords( keys );
+  keys.add("atoms","ATOMS","the pair of atom that we are calculating the distance between");
+  keys.addFlag("COMPONENTS",false,"calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z");  
+  keys.setValueDescription("scalar","the distance between the input atoms");
+}
+
+Distance::Distance(const ActionOptions&ao):
+PLUMED_COLVAR_INIT(ao),
+components(false),
+pbc(true)
+{
+  vector<AtomNumber> atoms;
+  parseAtomList("ATOMS",atoms);
+  if(atoms.size()!=2)
+    error("Number of specified atoms should be 2");
+  parseFlag("COMPONENTS",components);
+  bool nopbc=!pbc;
+  parseFlag("NOPBC",nopbc);
+  pbc=!nopbc;
+  checkRead();
+
+  log.printf("  between atoms %d %d\n",atoms[0].serial(),atoms[1].serial());
+  if(pbc) log.printf("  using periodic boundary conditions\n");
+  else    log.printf("  without periodic boundary conditions\n");
+
+
+  if(!components){
+
+    addValueWithDerivatives(); setNotPeriodic();
+
+  } else{
+    addComponentWithDerivatives("x"); componentIsNotPeriodic("x");
+    addComponentWithDerivatives("y"); componentIsNotPeriodic("y");
+    addComponentWithDerivatives("z"); componentIsNotPeriodic("z");
+  }
+
+  requestAtoms(atoms);
+}
+
+
+// calculator
+void Distance::calculate(){
+
+  Vector distance;
+  if(pbc){
+    distance=pbcDistance(getPosition(0),getPosition(1));
+  } else {
+    distance=delta(getPosition(0),getPosition(1));
+  }
+  const double value=distance.modulo();
+  const double invvalue=1.0/value;
+
+  if(!components){
+
+    setAtomsDerivatives(0,-invvalue*distance);
+    setAtomsDerivatives(1,invvalue*distance);
+    setBoxDerivatives  (-invvalue*Tensor(distance,distance));
+    setValue           (value);
+
+  }else{
+
+    Value* valuex=getPntrToComponent("x");
+    Value* valuey=getPntrToComponent("y");
+    Value* valuez=getPntrToComponent("z");
+
+    setAtomsDerivatives (valuex,0,Vector(-1,0,0));
+    setAtomsDerivatives (valuex,1,Vector(+1,0,0));
+    setBoxDerivatives   (valuex,Tensor(distance,Vector(-1,0,0)));
+    valuex->set(distance[0]);
+
+    setAtomsDerivatives (valuey,0,Vector(0,-1,0));
+    setAtomsDerivatives (valuey,1,Vector(0,+1,0));
+    setBoxDerivatives   (valuey,Tensor(distance,Vector(0,-1,0)));
+    valuey->set(distance[1]);
+
+    setAtomsDerivatives (valuez,0,Vector(0,0,-1));
+    setAtomsDerivatives (valuez,1,Vector(0,0,+1));
+    setBoxDerivatives   (valuez,Tensor(distance,Vector(0,0,-1)));
+    valuez->set(distance[2]);
+  };
+}
+
+}
+
+
+

tdata/tests.json

@@ -178,6 +178,13 @@
        "actions": ["DUMPATOMS"],
        "tooltips": ["DUMPATOMS", "ATOMS", "@ndx:", "FILE"],
        "badges": ["fail"]
+      },
+      {
+       "input": "#SETTINGS INPUTFILES=tdata/Distance2.cpp \nLOAD FILE=tdata/Distance2.cpp",
+       "index": 27,
+       "actions": ["LOAD"],
+       "tooltips": ["LOAD", "FILE", "tdata/Distance2.cpp"],
+       "badges": ["fail", "load"]
       }
    ]
 }