Merge branch 'v2.10'

developer-doc/AddingRegressionTests.md

@@ -49,18 +49,17 @@ extra_files="../../trajectories/diala_traj_nm.xyz  ../trajectories/path_msd/all.
 - The first line in this file - the one containing the string mpiprocs=2 - tells PLUMED that when this regtest should be run using MPI on two nodes.
 If mpiprocs is not specified then PLUMED will, by default, run the test one node.
 
-- The second line tells PLUMED that the test is to be performed using the command line tool <a href="../../user-doc/html/driver.html">driver</a>.  
-There are four options that you can use here:
-type=driver tells PLUMED to run the test by reading in a trajectory and analysing it using <a href="../../user-doc/html/driver.html">driver</a>, 
-type=simplemd tells PLUMED that the test will involve
-running some Lennard Jones MD using <a href="../../user-doc/html/simplemd.html">simplemd</a>, 
-type=sum_hills tells PLUMED that the test will involve summing gaussians using the 
-<a href="../../user-doc/html/sum_hills.html">sum_hills</a> untility
- and type=make tells PLUMED that a main function (called main.cpp) is included in the regtest directory and that the test should compile this function, link in
-the PLUMED library and run the resulting executible. The vast majority of features are best tested using type=driver here although the type=make function
-can be useful for testing tools that are used in many places in the code (see the code in regtest/basic/rt-make-4 for an example of how use type=make to test
-PLUMED's internal matrix class).  If you need to test PLUMED in a way that is not included in these various types please contact the PLUMED developers before
+- The second line tells PLUMED that the test is to be performed using the command line tool <a href="../../user-doc/html/driver.html">driver</a>.
+The vast majority of features are best tested using type=driver here although the type=make function can be useful for testing tools that are used in many places in the code (see the code in regtest/basic/rt-make-4 for an example of how use type=make to test PLUMED's internal matrix class).  If you need to test PLUMED in a way that is not included in these various types please contact the PLUMED developers before
 making any changes.
+There are four options that you can use here:
+    - type=driver tells PLUMED to run the test by reading in a trajectory and analysing it using <a href="../../user-doc/html/driver.html">driver</a>,
+    - type=simplemd tells PLUMED that the test will involve
+running some Lennard Jones MD using <a href="../../user-doc/html/simplemd.html">simplemd</a>,
+    - type=sum_hills tells PLUMED that the test will involve summing gaussians using the 
+<a href="../../user-doc/html/sum_hills.html">sum_hills</a> utility
+    - type=make tells PLUMED that a main function (called main.cpp) is included in the regtest directory and that the test should compile this function, link in
+the PLUMED library and run the resulting executible.
 
 - The third line - the one containing the string plumed_modules=adjmat - tells PLUMED that this regtest needs the optional module adjmat to be installed in 
 order for it to be run.  Before trying to run this test PLUMED will thus check whether or not the module is installed.  If it is not installed then it will 

regtest/.gitignore

@@ -43,6 +43,8 @@
 !/unittest
 !/wham
 !/metatensor
+!/sizeshape
+
 # These files we just want to ignore completely
 tmp
 report.txt

src/.gitignore

@@ -66,6 +66,7 @@
 !/membranefusion
 !/wham
 !/metatensor
+!/sizeshape
 
 # And just ignore these files
 *.xxd

src/bias/LWalls.cpp

@@ -35,10 +35,16 @@ The restraining potential starts acting on the system when the value of the CV i
 minus an offset \f$o_i\f$ (OFFSET).
 The expression for the bias due to the wall is given by:
 
+for UPPER_WALLS:
 \f$
   \sum_i {k_i}((x_i-a_i+o_i)/s_i)^e_i
 \f$
 
+for LOWER_WALLS:
+\f$
+  \sum_i {k_i}|(x_i-a_i-o_i)/s_i|^e_i
+\f$
+
 \f$k_i\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s_i\f$ (EPS) a rescaling factor and
 \f$e_i\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFFSET = 0.
 
@@ -143,7 +149,7 @@ void LWalls::calculate() {
     if( lscale < 0.) {
       const double k=kappa[i];
       const double exponent=exp[i];
-      double power = std::pow( lscale, exponent );
+      double power = std::pow( -lscale, exponent );
       f = -( k / epsilon ) * exponent * power / lscale;
       ene += k * power;
       totf2 += f * f;

src/bias/UWalls.cpp

@@ -35,10 +35,16 @@ The restraining potential starts acting on the system when the value of the CV i
 minus an offset \f$o_i\f$ (OFFSET).
 The expression for the bias due to the wall is given by:
 
+for UPPER_WALLS:
 \f$
   \sum_i {k_i}((x_i-a_i+o_i)/s_i)^e_i
 \f$
 
+for LOWER_WALLS:
+\f$
+  \sum_i {k_i}|(x_i-a_i-o_i)/s_i|^e_i
+\f$
+
 \f$k_i\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s_i\f$ (EPS) a rescaling factor and
 \f$e_i\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFFSET = 0.