Merge branch 'v2.0'

CHANGES/v2.0.txt

@@ -18,11 +18,15 @@ In addition, it is now much easier to contribute new functionality to the code b
 - Developer and user documentation 
 
 Version 2.0.1 (unpublised yet, check out branch v2.0 on git repository)
+
 For users:
 - Several small fixes in documentation and log file
+- Fixed a bug in HISTOGRAM with REWEIGHT_BIAS. Reweighting was only done when also temperature-reweighing was enabled.
 - Added message when "plumed simpled" is used on a non-existing file
+
 For developers:
 - Several small fixes in documentation
 - Added possibility to setup replica exchange from MD codes in fortran (commands "GREX setMPIFIntercomm" and "GREX setMPIFIntracomm")
+- cmd("setStopFlag") should now be called after PLUMED initialization.
 
 */

regtest/analysis/rt0/Makefile

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

regtest/analysis/rt0/config

+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz"

regtest/analysis/rt0/histoA.reference

+#! FIELDS x probs
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x  101
+#! SET periodic_x false
+   0.0000   0.0000
+   0.0300   0.0000
+   0.0600   0.0000
+   0.0900   0.0000
+   0.1200   0.0000
+   0.1500   0.0000
+   0.1800   0.0000
+   0.2100   0.0000
+   0.2400   0.0000
+   0.2700   0.0000
+   0.3000   0.0000
+   0.3300   0.0000
+   0.3600   0.0000
+   0.3900   0.0000
+   0.4200   0.0000
+   0.4500   0.0000
+   0.4800   0.0000
+   0.5100   0.0000
+   0.5400   0.0000
+   0.5700   0.0000
+   0.6000   0.0000
+   0.6300   0.0000
+   0.6600   0.0000
+   0.6900   0.0000
+   0.7200   0.0000
+   0.7500   0.0000
+   0.7800   0.0000
+   0.8100   0.0000
+   0.8400   0.0000
+   0.8700   0.0000
+   0.9000   0.0000
+   0.9300   0.0000
+   0.9600   0.0000
+   0.9900   0.0000
+   1.0200   0.0000
+   1.0500   0.0000
+   1.0800   0.0000
+   1.1100   0.0000
+   1.1400   0.0031
+   1.1700   0.0086
+   1.2000   0.0221
+   1.2300   0.0521
+   1.2600   0.1119
+   1.2900   0.2199
+   1.3200   0.3947
+   1.3500   0.6476
+   1.3800   0.9709
+   1.4100   1.3304
+   1.4400   1.6661
+   1.4700   1.9069
+   1.5000   1.9947
+   1.5300   1.9069
+   1.5600   1.6661
+   1.5900   1.3304
+   1.6200   0.9724
+   1.6500   0.6520
+   1.6800   0.4067
+   1.7100   0.2497
+   1.7400   0.1799
+   1.7700   0.1937
+   1.8000   0.2921
+   1.8300   0.4788
+   1.8600   0.7517
+   1.8900   1.0893
+   1.9200   1.4485
+   1.9500   1.7603
+   1.9800   1.9552
+   2.0100   1.9848
+   2.0400   1.8414
+   2.0700   1.5613
+   2.1000   1.2099
+   2.1300   0.8568
+   2.1600   0.5546
+   2.1900   0.3281
+   2.2200   0.1774
+   2.2500   0.0876
+   2.2800   0.0396
+   2.3100   0.0163
+   2.3400   0.0062
+   2.3700   0.0000
+   2.4000   0.0000
+   2.4300   0.0000
+   2.4600   0.0000
+   2.4900   0.0000
+   2.5200   0.0000
+   2.5500   0.0000
+   2.5800   0.0000
+   2.6100   0.0000
+   2.6400   0.0000
+   2.6700   0.0000
+   2.7000   0.0000
+   2.7300   0.0000
+   2.7600   0.0000
+   2.7900   0.0000
+   2.8200   0.0000
+   2.8500   0.0000
+   2.8800   0.0000
+   2.9100   0.0000
+   2.9400   0.0000
+   2.9700   0.0000
+   3.0000   0.0000

regtest/analysis/rt0/histoB.reference

+#! FIELDS x probs
+#! SET min_x 0.0
+#! SET max_x 3.0
+#! SET nbins_x  101
+#! SET periodic_x false
+   0.0000   0.0000
+   0.0300   0.0000
+   0.0600   0.0000
+   0.0900   0.0000
+   0.1200   0.0000
+   0.1500   0.0000
+   0.1800   0.0000
+   0.2100   0.0000
+   0.2400   0.0000
+   0.2700   0.0000
+   0.3000   0.0000
+   0.3300   0.0000
+   0.3600   0.0000
+   0.3900   0.0000
+   0.4200   0.0000
+   0.4500   0.0000
+   0.4800   0.0000
+   0.5100   0.0000
+   0.5400   0.0000
+   0.5700   0.0000
+   0.6000   0.0000
+   0.6300   0.0000
+   0.6600   0.0000
+   0.6900   0.0000
+   0.7200   0.0000
+   0.7500   0.0000
+   0.7800   0.0000
+   0.8100   0.0000
+   0.8400   0.0000
+   0.8700   0.0000
+   0.9000   0.0000
+   0.9300   0.0000
+   0.9600   0.0000
+   0.9900   0.0000
+   1.0200   0.0000
+   1.0500   0.0000
+   1.0800   0.0000
+   1.1100   0.0000
+   1.1400   0.0027
+   1.1700   0.0077
+   1.2000   0.0199
+   1.2300   0.0469
+   1.2600   0.1008
+   1.2900   0.1979
+   1.3200   0.3553
+   1.3500   0.5829
+   1.3800   0.8740
+   1.4100   1.1975
+   1.4400   1.4997
+   1.4700   1.7165
+   1.5000   1.7954
+   1.5300   1.7165
+   1.5600   1.4997
+   1.5900   1.1975
+   1.6200   0.8756
+   1.6500   0.5877
+   1.6800   0.3684
+   1.7100   0.2307
+   1.7400   0.1755
+   1.7700   0.2027
+   1.8000   0.3169
+   1.8300   0.5250
+   1.8600   0.8262
+   1.8900   1.1981
+   1.9200   1.5931
+   1.9500   1.9362
+   1.9800   2.1505
+   2.0100   2.1830
+   2.0400   2.0253
+   2.0700   1.7172
+   2.1000   1.3307
+   2.1300   0.9424
+   2.1600   0.6100
+   2.1900   0.3609
+   2.2200   0.1951
+   2.2500   0.0964
+   2.2800   0.0435
+   2.3100   0.0180
+   2.3400   0.0068
+   2.3700   0.0000
+   2.4000   0.0000
+   2.4300   0.0000
+   2.4600   0.0000
+   2.4900   0.0000
+   2.5200   0.0000
+   2.5500   0.0000
+   2.5800   0.0000
+   2.6100   0.0000
+   2.6400   0.0000
+   2.6700   0.0000
+   2.7000   0.0000
+   2.7300   0.0000
+   2.7600   0.0000
+   2.7900   0.0000
+   2.8200   0.0000
+   2.8500   0.0000
+   2.8800   0.0000
+   2.9100   0.0000
+   2.9400   0.0000
+   2.9700   0.0000
+   3.0000   0.0000

regtest/analysis/rt0/plumed.dat

+x: DISTANCE ATOMS=1,2
+
+RESTRAINT ARG=x SLOPE=1.0 AT=0.0
+
+HISTOGRAM ... 
+  ARG=x
+  TEMP=300
+  GRID_MIN=0.0
+  GRID_MAX=3.0
+  GRID_BIN=100
+  BANDWIDTH=0.1
+  GRID_WFILE=histoA
+  FMT=%8.4f
+  RUN=1
+... HISTOGRAM
+
+HISTOGRAM ...
+  ARG=x
+  TEMP=300
+  GRID_MIN=0.0
+  GRID_MAX=3.0
+  GRID_BIN=100
+  BANDWIDTH=0.1
+  GRID_WFILE=histoB
+  FMT=%8.4f
+  REWEIGHT_BIAS
+  RUN=1
+... HISTOGRAM
+
+
+

regtest/analysis/rt0/trajectory.xyz

+2
+0 0 0
+X 0 0 0
+X 0 0 1
+2
+0 0 0
+X 0 0 0
+X 0 0 1.5
+2
+0 0 0
+X 0 0 0
+X 0 0 2

src/analysis/Analysis.cpp

@@ -222,9 +222,9 @@ void Analysis::calculate(){
      double energy=plumed.getAtoms().getEnergy()+bias;
      // Reweighting because of temperature difference
      ww=-( (1.0/rtemp) - (1.0/simtemp) )*(energy+bias) / plumed.getAtoms().getKBoltzmann();
-     // Reweighting because of biases
-     if( !biases.empty() ) ww += bias/( plumed.getAtoms().getKBoltzmann()*simtemp );
   }
+  // Reweighting because of biases
+  if( !biases.empty() ) ww += bias/( plumed.getAtoms().getKBoltzmann()*simtemp );
 
   if(single_run){
      // Get the arguments and store them in a vector of vectors

src/cltools/Driver.cpp

@@ -256,8 +256,6 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
   int rr=sizeof(real);
   p.cmd("setRealPrecision",&rr);
   int checknatoms=-1;
-  int plumedStopCondition=0;
-  p.cmd("setStopFlag",&plumedStopCondition);
   int step=0;
   if(Communicator::initialized()){
     if(multi){
@@ -327,7 +325,7 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
   while(true){
     if(!noatoms){
        if(!Tools::getline(fp,line)) break;
-    } else if ( plumedStopCondition ) break;
+    }
 
     int natoms;
     bool first_step=false;
@@ -421,7 +419,9 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
       }
     }
 
+    int plumedStopCondition=0;
     p.cmd("setStep",&step);
+    p.cmd("setStopFlag",&plumedStopCondition);
     if(!noatoms){
        if(trajectory_fmt=="xyz"){
          if(!Tools::getline(fp,line)) error("premature end of trajectory file");
@@ -559,6 +559,8 @@ int Driver<real>::main(FILE* in,FILE*out,Communicator& pc){
        fprintf(fp_forces,fmt.c_str(),forces[3*i],forces[3*i+1],forces[3*i+2]);
    }
 
+    if(noatoms && plumedStopCondition) break;
+
     step+=stride;
   }
   p.cmd("runFinalJobs");

src/core/PlumedMain.cpp

@@ -289,11 +289,11 @@ void PlumedMain::cmd(const std::string & word,void*val){
        CHECK_NOTINIT(initialized,word);
        CHECK_NULL(val,word);
        log.open(static_cast<char*>(val),"w");
+// other commands that should be used after initialization:
   } else if(word=="setStopFlag"){
-       CHECK_NOTINIT(initialized,word);
+       CHECK_INIT(initialized,word);
        CHECK_NULL(val,word);
        stopFlag=static_cast<int*>(val);
-// other commands that should be used after initialization:
   } else if(word=="getExchangesFlag"){
        CHECK_INIT(initialized,word);
        CHECK_NULL(val,word);

user-doc/Installation.txt

@@ -7,7 +7,7 @@
 PLUMED does not yet have any automatic configuration procedure and most of the 
 decisions should be taken by the user. As a first step configure with the command:
 \verbatim
-> ./configure
+> ./configure.sh
 \endverbatim
 
 You will have to choose among a set of available preconfigured files.