Merge pull request plumed#949 from Iximiel/warningToMklib

Proposal for mklib.sh modification

regtest/basic/rt15bis-legacyIncludeWarning/COLVAR.reference

@@ -0,0 +1,3 @@
+#! FIELDS time d2
+ 0.000000 1.000000
+ 0.050000 9.000000

regtest/basic/rt15bis-legacyIncludeWarning/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"
+//all the shortcuts to ActionRegister were removed and it should only be included by core/ActionRegister.h
+#include "colvar/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");  
+}
+
+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]);
+  };
+}
+
+}
+
+
+

regtest/basic/rt15bis-legacyIncludeWarning/Distance2.cpp.reference

@@ -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"
+//all the shortcuts to ActionRegister were removed and it should only be included by core/ActionRegister.h
+#include "colvar/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");  
+}
+
+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]);
+  };
+}
+
+}
+
+
+

regtest/basic/rt15bis-legacyIncludeWarning/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/basic/rt15bis-legacyIncludeWarning/config

@@ -0,0 +1,8 @@
+type=driver
+plumed_needs="dlopen"
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz"
+
+
+function plumed_regtest_after(){
+	grep "WARNING: using a legacy ActionRegister" err > errorParsed
+}

regtest/basic/rt15bis-legacyIncludeWarning/der2

@@ -0,0 +1,2 @@
+works like rt15, but emulates an old include statement style for ActionRegister.h
+Distance2.cpp reference is set up because mklib should NOT change the inputfile

regtest/basic/rt15bis-legacyIncludeWarning/errorParsed.reference

@@ -0,0 +1 @@
+WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">>

regtest/basic/rt15bis-legacyIncludeWarning/plumed.dat

@@ -0,0 +1,8 @@
+# This is loading a collective variable on the fly:
+LOAD FILE=Distance2.cpp
+
+d2: DISTANCE2 ATOMS=1,2
+
+PRINT FILE=COLVAR ARG=d2
+
+ENDPLUMED

regtest/basic/rt15bis-legacyIncludeWarning/trajectory.xyz

@@ -0,0 +1,20 @@
+8
+10 0 0 0 10 0 0 0 10
+X 0.5 0.5 0.5
+X 0.5 0.5 9.5
+X 0.5 9.5 0.5
+X 0.5 9.5 9.5
+X 9.5 0.5 0.5
+X 9.5 0.5 9.5
+X 9.5 9.5 0.5
+X 9.5 9.5 9.5
+8
+10 10 0 0 10 10 10 0 10
+X 0.5 0.5 0.5
+X 0.5 0.5 9.5
+X 0.5 9.5 0.5
+X 0.5 9.5 9.5
+X 9.5 0.5 0.5
+X 9.5 0.5 9.5
+X 9.5 9.5 0.5
+X 9.5 9.4 9.5

scripts/mklib.sh

@@ -29,14 +29,28 @@ then
   echo "ERROR: I cannot find file $file"
   exit 1
 fi
+#adding a simple tmpfile, to preprocess "in place" the input file,
+#this assumes the user has write permission in the current directory
+#which should be true since we are going to compile and output something here
+tmpfile=$(mktemp ${file%.cpp}.XXXXXX.cpp)
+cp "${file}" "${tmpfile}"
+
+if grep -q '^#include "\(bias\|colvar\|function\|sasa\|vatom\)\/ActionRegister.h"' "${tmpfile}"; then
+   >&2 echo 'WARNING: using a legacy ActionRegister.h include path, please use <<#include "core/ActionRegister.h">>'
+   sed -i.bak 's%^#include ".*/ActionRegister.h"%#include "core/ActionRegister.h"%g' "${tmpfile}"
+fi
+
+if grep -q '^#include "\(cltools\)\/CLToolRegister.h"' "${tmpfile}"; then
+   >&2  echo 'WARNING: using a legacy  CLToolRegister.h include path, please use <<#include "core/CLToolRegister.h">>'
+   sed -i.bak 's%^#include ".*/CLToolRegister.h"%#include "core/CLToolRegister.h"%g' "${tmpfile}"
+fi
 
 rm -f "$obj" "$lib"
 
 if test "$PLUMED_IS_INSTALLED" = yes ; then
-  eval "$compile" "$obj" "$file" && eval "$link_installed" "$lib" "$obj"
+  eval "$compile" "$obj" "$tmpfile" && eval "$link_installed" "$lib" "$obj"
 else
-  eval "$compile" "$obj" "$file" && eval "$link_uninstalled" "$lib" "$obj"
+  eval "$compile" "$obj" "$tmpfile" && eval "$link_uninstalled" "$lib" "$obj"
 fi
 
-
-
+rm -f ${tmpfile} ${tmpfile}.bak