From a2186af7f41666acacf76a67073f378248d8b67e Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 8 Aug 2013 17:20:16 +0200
Subject: [PATCH] Added regtest for LOAD
---
regtest/basic/rt15/COLVAR.reference | 3 +
regtest/basic/rt15/Distance2.cpp | 130 ++++++++++++++++++++++++++++
regtest/basic/rt15/Makefile | 1 +
regtest/basic/rt15/config | 3 +
regtest/basic/rt15/der2 | 1 +
regtest/basic/rt15/plumed.dat | 8 ++
regtest/basic/rt15/trajectory.xyz | 20 +++++
7 files changed, 166 insertions(+)
create mode 100644 regtest/basic/rt15/COLVAR.reference
create mode 100644 regtest/basic/rt15/Distance2.cpp
create mode 100644 regtest/basic/rt15/Makefile
create mode 100644 regtest/basic/rt15/config
create mode 100644 regtest/basic/rt15/der2
create mode 100644 regtest/basic/rt15/plumed.dat
create mode 100644 regtest/basic/rt15/trajectory.xyz
diff --git a/regtest/basic/rt15/COLVAR.reference b/regtest/basic/rt15/COLVAR.reference
new file mode 100644
index 000000000..a95e7f5e5
--- /dev/null
+++ b/regtest/basic/rt15/COLVAR.reference
@@ -0,0 +1,3 @@
+#! FIELDS time d2
+ 0.000000 1.000000
+ 0.050000 9.000000
diff --git a/regtest/basic/rt15/Distance2.cpp b/regtest/basic/rt15/Distance2.cpp
new file mode 100644
index 000000000..3ff1f3562
--- /dev/null
+++ b/regtest/basic/rt15/Distance2.cpp
@@ -0,0 +1,130 @@
+/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+ 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");
+}
+
+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]);
+ };
+}
+
+}
+
+
+
diff --git a/regtest/basic/rt15/Makefile b/regtest/basic/rt15/Makefile
new file mode 100644
index 000000000..3703b27ce
--- /dev/null
+++ b/regtest/basic/rt15/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/basic/rt15/config b/regtest/basic/rt15/config
new file mode 100644
index 000000000..4d3237ab4
--- /dev/null
+++ b/regtest/basic/rt15/config
@@ -0,0 +1,3 @@
+type=driver
+plumed_needs="dlopen"
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz"
diff --git a/regtest/basic/rt15/der2 b/regtest/basic/rt15/der2
new file mode 100644
index 000000000..c7900cb65
--- /dev/null
+++ b/regtest/basic/rt15/der2
@@ -0,0 +1 @@
+fake file just to test backup
diff --git a/regtest/basic/rt15/plumed.dat b/regtest/basic/rt15/plumed.dat
new file mode 100644
index 000000000..408583cf1
--- /dev/null
+++ b/regtest/basic/rt15/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
diff --git a/regtest/basic/rt15/trajectory.xyz b/regtest/basic/rt15/trajectory.xyz
new file mode 100644
index 000000000..aa856131c
--- /dev/null
+++ b/regtest/basic/rt15/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
--
GitLab