diff --git a/CHANGES/v2.0.txt b/CHANGES/v2.0.txt
index fd0399275d30424cb4106d243e25a97688b0042c..54ba4606daecd834585eedd6b96a0fd7e7ea33e2 100644
--- a/CHANGES/v2.0.txt
+++ b/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.
*/
diff --git a/regtest/analysis/rt0/Makefile b/regtest/analysis/rt0/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..3703b27cea227aa053fb6d1d73f861e4384dbcee
--- /dev/null
+++ b/regtest/analysis/rt0/Makefile
@@ -0,0 +1 @@
+include ../../scripts/test.make
diff --git a/regtest/analysis/rt0/config b/regtest/analysis/rt0/config
new file mode 100644
index 0000000000000000000000000000000000000000..f93ec1a97465724691bf162d4735f5ea3648bbb4
--- /dev/null
+++ b/regtest/analysis/rt0/config
@@ -0,0 +1,3 @@
+type=driver
+# this is to test a different name
+arg="--plumed plumed.dat --ixyz trajectory.xyz"
diff --git a/regtest/analysis/rt0/histoA.reference b/regtest/analysis/rt0/histoA.reference
new file mode 100644
index 0000000000000000000000000000000000000000..11425019a9f1aa584941f61388daf5301c3fbaac
--- /dev/null
+++ b/regtest/analysis/rt0/histoA.reference
@@ -0,0 +1,106 @@
+#! 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
diff --git a/regtest/analysis/rt0/histoB.reference b/regtest/analysis/rt0/histoB.reference
new file mode 100644
index 0000000000000000000000000000000000000000..0facce1f608dbfad4d6f637ce120bf88ab7d1794
--- /dev/null
+++ b/regtest/analysis/rt0/histoB.reference
@@ -0,0 +1,106 @@
+#! 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
diff --git a/regtest/analysis/rt0/plumed.dat b/regtest/analysis/rt0/plumed.dat
new file mode 100755
index 0000000000000000000000000000000000000000..e7911eceaebf9144adf44cccb3d30c3a4ffa8610
--- /dev/null
+++ b/regtest/analysis/rt0/plumed.dat
@@ -0,0 +1,31 @@
+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
+
+
+
diff --git a/regtest/analysis/rt0/trajectory.xyz b/regtest/analysis/rt0/trajectory.xyz
new file mode 100644
index 0000000000000000000000000000000000000000..c910ae5c6fda2241cfe5be857f9b8493db430ed3
--- /dev/null
+++ b/regtest/analysis/rt0/trajectory.xyz
@@ -0,0 +1,12 @@
+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
diff --git a/src/analysis/Analysis.cpp b/src/analysis/Analysis.cpp
index 15e0e0936c8437427ce5ba0d1eac43dcc372c7a5..d78a42337e5af3aeb763070849742d665a6604ed 100644
--- a/src/analysis/Analysis.cpp
+++ b/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
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index 639dfb99ca325871f21ad0bd6713bf87f3f26dc3..74b0a0e6f031b6a1c718bb527885455ad40b3a3d 100644
--- a/src/cltools/Driver.cpp
+++ b/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");
diff --git a/src/core/PlumedMain.cpp b/src/core/PlumedMain.cpp
index db21f28601dbba4b076ea41a4aa0b41c61948648..b33cd6fe739d189c310de890fc377b4b60681f1d 100644
--- a/src/core/PlumedMain.cpp
+++ b/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);
diff --git a/user-doc/Installation.txt b/user-doc/Installation.txt
index 883c8c0fb61962fb0a2a2763079265f355f01685..da5a75ccda03b5575ee9efadc37d4c191013fa73 100644
--- a/user-doc/Installation.txt
+++ b/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.