Merge branch 'v2.1'

CHANGES/v2.1.txt

@@ -190,6 +190,8 @@ For users:
 - Fixed a bug in the virial computed with \ref FIT_TO_TEMPLATE when the reference pdb had center non located at the origin.
 - Fixed a bug in the the forces computed with \ref FIT_TO_TEMPLATE when used in combination with \ref COM, \ref CENTER, or \ref GHOST
 - Fixed a bug that could lead plumed to be stuck with domain decomposition in some extreme case (one domain with all atoms, other domains empty).
+- Fixed a bug when \ref COMBINE or \ref MATHEVAL are used with PERIODIC keyword. Now when PERIODIC keyword is used the result
+  of the calculation is brought within the periodicity domain. See <a href="http://github.com/plumed/plumed2/issues/139"> here </a>.
 - Fixed a bug related to \RANDOM_EXCHANGES followed by \ref INCLUDE
 - Updated internal molfile plugins to VMD 1.9.2.
 - Included crd and crdbox formats to internal molfile.

regtest/basic/rt-combine-periodic/Makefile

+include ../../scripts/test.make

regtest/basic/rt-combine-periodic/colvar.reference

+#! FIELDS time a1 a2 p1 p2 pa1 pa2 pa1m pa2m
+#! SET min_p1 -pi
+#! SET max_p1 pi
+#! SET min_p2 -pi
+#! SET max_p2 pi
+#! SET min_pa1m -pi
+#! SET max_pa1m pi
+#! SET min_pa2m -pi
+#! SET max_pa2m pi
+ 0.000000 -1.22173 2.61799 -1.66697 3.13967 -0.445236 0.521676 -0.445236 0.521676
+ 0.050000 -1.22173 2.61799 -1.68457 -3.1278 -0.462839 -5.74579 -0.462839 0.537394

regtest/basic/rt-combine-periodic/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz tmp.xyz --dump-forces forces --dump-forces-fmt=%8.4f"

regtest/basic/rt-combine-periodic/plumed.dat

+# some point "a" in phi/psi space
+a1: CONSTANT VALUE=-1.22173047639603070385 #-70
+a2: CONSTANT VALUE=2.61799387799149436539  #150
+# current point "p" in phi-psi space
+p1: TORSION ATOMS=5,7,9,15
+p2: TORSION ATOMS=7,9,15,17
+
+# p-a vector
+pa1: COMBINE ARG=p1,a1 COEFFICIENTS=1.,-1. PERIODIC=NO
+pa2: COMBINE ARG=p2,a2 COEFFICIENTS=1.,-1. PERIODIC=NO
+
+#trying to get a periodic p-a vector
+pa1m: COMBINE ARG=pa1 COEFFICIENTS=1. PERIODIC=-pi,pi 
+pa2m: COMBINE ARG=pa2 COEFFICIENTS=1. PERIODIC=-pi,pi 
+
+PRINT ARG=a1,a2,p1,p2,pa1,pa2,pa1m,pa2m  STRIDE=1 FMT=%g FILE=colvar
+

regtest/basic/rt-combine-periodic/tmp.xyz

+22
+ generated by VMD
+ C         7.426660        1.175157        5.521920
+ H         7.826973        0.198052        5.201265
+ H         6.701839        1.373954        4.710052
+ H         6.852031        1.068966        6.450162
+ C         8.491815        2.219806        5.666954
+ O         9.204520        2.159070        4.639861
+ N         8.627721        3.240756        6.604086
+ H         8.070031        3.064171        7.411407
+ C         9.705361        4.297344        6.626343
+ H         9.972519        4.030229        5.608061
+ C         9.122450        5.787033        6.539737
+ H         9.974642        6.390628        6.198587
+ H         8.773165        6.213179        7.495877
+ H         8.400371        5.922006        5.680896
+ C        10.867927        4.068889        7.454099
+ O        10.797208        3.139278        8.218799
+ N        11.849608        5.051494        7.459472
+ H        11.425094        5.790774        6.972304
+ C        13.055787        4.954424        8.148125
+ H        13.163018        4.103357        8.702283
+ H        13.204816        5.877514        8.754676
+ H        13.846210        5.023830        7.438193
+22
+ generated by VMD
+ C         7.424259        1.175460        5.521116
+ H         7.835259        0.209655        5.175528
+ H         6.705950        1.400984        4.719906
+ H         6.868944        1.071771        6.471955
+ C         8.498229        2.230016        5.672456
+ O         9.202964        2.162216        4.644840
+ N         8.626006        3.241682        6.614517
+ H         8.095504        3.061236        7.451256
+ C         9.713079        4.300539        6.617662
+ H         9.974644        4.047624        5.600792
+ C         9.123056        5.776693        6.541171
+ H         9.995579        6.372286        6.197186
+ H         8.749353        6.196899        7.491727
+ H         8.418746        5.948982        5.668446
+ C        10.866976        4.075941        7.446161
+ O        10.793647        3.133207        8.213814
+ N        11.839444        5.045859        7.457207
+ H        11.427945        5.823356        6.979874
+ C        13.060909        4.959161        8.150963
+ H        13.153873        4.067696        8.730364
+ H        13.182820        5.891395        8.753601
+ H        13.859556        5.012844        7.405939

regtest/basic/rt44/config

 type=sum_hills
 # this is to test a different name
-arg=" --min -pi,pi --max -pi,pi --bin 99,99 --hills HILLS_t1 "
+arg=" --min -pi,pi --max -pi,pi --bin 99,99 --hills HILLS_t1 --fmt %12.7f"
 extra_files="../../trajectories/HILLS_t1"

src/core/Value.h

@@ -82,6 +82,8 @@ private:
   double inv_max_minus_min;
 /// Complete the setup of the periodicity
   void setupPeriodicity();
+// bring value within PBCs
+  void applyPeriodicity();
 public:
 /// A constructor that can be used to make Vectors of values
   Value();
@@ -148,6 +150,14 @@ void copy( const Value& val1, Value& val2 );
 void copy( const Value& val1, Value* val2 );
 void add( const Value& val1, Value* valout );
 
+inline
+void Value::applyPeriodicity(){
+  if(periodicity==periodic){
+    value=min+difference(min,value);
+    if(value<min)value+=max_minus_min;
+  }
+}
+
 inline
 void product( const Value& val1, const Value& val2, Value& valout ){
   plumed_assert( val1.derivatives.size()==val2.derivatives.size() );
@@ -176,12 +186,14 @@ inline
 void Value::set(double v){
   value_set=true;
   value=v;
+  applyPeriodicity();
 }
 
 inline
 void Value::add(double v){
   value_set=true;
   value+=v;
+  applyPeriodicity();
 }
 
 inline