Cluster move: larger clusters allowed but limited to translation, only.

Travis script cleanup

Author: mlund

.travis.yml

@@ -1,5 +1,5 @@
 language: cpp
-dist: xenial # trusty
+dist: xenial
 sudo: required
 group: edge
 compiler: clang
@@ -14,11 +14,6 @@ matrix:
   # Linux / Clang
   - os: linux
     env: [COMPILER=clang++, CXX=clang++, CC=clang]
-    #env: [COMPILER=clang++-5.0, CXX=clang++, CC=clang]
-    #addons:
-    #  apt:
-    #    sources: ['ubuntu-toolchain-r-test', 'llvm-toolchain-trusty-5.0']
-    #    packages: ['g++-7', 'clang-5.0']
 
 install:
   - |
@@ -39,17 +34,6 @@ install:
 
 script:
   - |
-    if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then
-      #conda install cmake openmpi=1.6.3 python=3
-      #  CXX=clang++ CC=clang cmake . -DENABLE_MPI=on
-      #  make faunus
-      #  make tests
-      #  make test
-      cd scripts/
-      conda config --set anaconda_upload yes
-      conda-build --user teokem --token "${CONDA_UPLOAD_TOKEN}" .
-    else
-      cd scripts/
-      conda config --set anaconda_upload yes
-      conda-build --user teokem --token "${CONDA_UPLOAD_TOKEN}" .
-    fi
+    cd scripts/
+    conda config --set anaconda_upload yes
+    conda-build --user teokem --token "${CONDA_UPLOAD_TOKEN}" .

CMakeLists.txt

@@ -386,6 +386,7 @@ install(FILES
     ${CMAKE_SOURCE_DIR}/examples/README.md
     ${CMAKE_SOURCE_DIR}/examples/bulk.yml
     ${CMAKE_SOURCE_DIR}/examples/cluster.yml
+    ${CMAKE_SOURCE_DIR}/examples/cluster.agr
     ${CMAKE_SOURCE_DIR}/examples/cluster.out.json
     ${CMAKE_SOURCE_DIR}/examples/cluster.state.json
     ${CMAKE_SOURCE_DIR}/examples/seawater.yml
@@ -402,6 +403,7 @@ install(FILES
     ${CMAKE_SOURCE_DIR}/examples/membrane.state.json
     ${CMAKE_SOURCE_DIR}/examples/lipid.xyz
     ${CMAKE_SOURCE_DIR}/examples/penalty.yml
+    ${CMAKE_SOURCE_DIR}/examples/penalty.ipynb
     ${CMAKE_SOURCE_DIR}/examples/pythontest.py
     ${CMAKE_SOURCE_DIR}/examples/isochoric.yml
     ${CMAKE_SOURCE_DIR}/examples/isochoric.xyz

examples/README.md

@@ -5,12 +5,14 @@ demonstrating features of Faunus. It is assumed that Faunus has
 already been installed.
 
 Example         | Description
---------------- | --------------------------------------------------------
+--------------- | ---------------------------------------------------------
+`bulk`          | Melted NaCl using Ewald summation and isobaric moves
+`cluster`       | Illustration of molecular cluster moves
 `isochoric`     | Bending modulus via penalty function and isochoric moves
 `membrane`      | Coarse-grained lipid bilayer under zero tension
 `minimal`       | A simple Lennard-Jones particle system
-`penalty`       | Wang-Landau sampling along a 2D reaction coordinate
-`water`         | SPC/E water using Ewald or other electrostatic methods
+`penalty`       | 2D Wang-Landau - see also Jupyter Notebook
+`water`         | SPC/E water in the NPT ensemble
 
 Each example consists of a YAML input file and, potentially,
 other files such as previously generated states (`.state.json`) or

examples/water.yml

@@ -1,5 +1,5 @@
 temperature: 300
-random: {seed: default}
+random: {seed: fixed}
 geometry: {length: 18.6}
 mcloop: {macro: 10, micro: 100}
 
@@ -17,7 +17,7 @@ energy:
     - isobaric: {P/atm: 1}
     - nonbonded_coulomblj:
         lennardjones: {mixing: LB}
-        coulomb: {type: fanourgakis, epsr: 1, cutoff: 9, alpha: 0.21, kcutoff: 7.3}
+        coulomb: {type: fanourgakis, epsr: 1, cutoff: 9}
         cutoff_g2g: 10
 
 moves:

scripts/meta.yaml

@@ -13,15 +13,13 @@ requirements:
     - librsvg
     - numpy
     - matplotlib
-    #- cmake >=3.9
     - python {{ python }}
     - ruamel_yaml
     - nbconvert
     - notebook
     - jupyter
     - openmpi 1.6.3      # [osx]
     - openmpi 3.1.*      # [linux64]
-    #- clangdev >=5       # [linux64]
     #- pandoc >=1.19 # [linux64]
   run:
     - openmpi 1.6.3 # [osx]

src/move.h

@@ -759,6 +759,7 @@ namespace Faunus {
                     Average<double> msqd, msqd_angle, N;
                     double thresholdsq=0, dptrans=0, dprot=0, angle=0, _bias=0;
                     size_t bias_rejected=0;
+                    bool rotate; // true if cluster should be rotated
                     Point dir={1,1,1}, dp;
                     std::vector<std::string> names; // names of molecules to be considered
                     std::vector<int> ids; // molecule id's of molecules to be considered
@@ -804,7 +805,7 @@ namespace Faunus {
                      * @param first Index of initial molecule (randomly selected)
                      * @param index w. all molecules clustered around first (first included)
                      */
-                    void findCluster(Tspace &spc, size_t first, std::set<size_t>& cluster) const {
+                    void findCluster(Tspace &spc, size_t first, std::set<size_t>& cluster) {
                         assert(first < spc.p.size());
                         std::set<size_t> pool(index.begin(), index.end());
                         assert(pool.count(first)>0);
@@ -838,11 +839,13 @@ namespace Faunus {
                             for (auto j : cluster)
                                 if (j>i)
                                     if (spc.geo.sqdist(spc.groups.at(i).cm, spc.groups.at(j).cm)>=max*max)
-                                        throw std::runtime_error(name+": cluster larger than half box length");
+                                        rotate=false; // skip rotation if cluster larger than half the box length
                     }
 
                     void _move(Change &change) override {
-                        if (thresholdsq>0 && !index.empty()) {
+                        _bias=0;
+                        rotate=true;
+                        if (thresholdsq>0 and not index.empty()) {
                             std::set<size_t> cluster; // all group index in cluster
                             size_t first = *slump.sample(index.begin(), index.end()); // random molecule (nuclei)
                             findCluster(spc, first, cluster); // find cluster around first
@@ -852,6 +855,8 @@ namespace Faunus {
                             d.all=true;
                             dp = 0.5*ranunit(slump).cwiseProduct(dir) * dptrans;
                             angle = dprot * (slump()-0.5);
+                            if (not rotate)
+                                angle=0;
 
                             Point COM = Geometry::trigoCom(spc, cluster); // cluster center
                             Eigen::Quaterniond Q;
@@ -860,11 +865,13 @@ namespace Faunus {
                             for (auto i : cluster) { // loop over molecules in cluster
                                 auto &g = spc.groups[i];
 
-                                Geometry::rotate(g.begin(), g.end(), Q, spc.geo.boundaryFunc, -COM);
-                                g.cm = g.cm-COM;
-                                spc.geo.boundary(g.cm);
-                                g.cm = Q*g.cm+COM;
-                                spc.geo.boundary(g.cm);
+                                if (rotate) {
+                                    Geometry::rotate(g.begin(), g.end(), Q, spc.geo.boundaryFunc, -COM);
+                                    g.cm = g.cm-COM;
+                                    spc.geo.boundary(g.cm);
+                                    g.cm = Q*g.cm+COM;
+                                    spc.geo.boundary(g.cm);
+                                }
 
                                 g.translate( dp, spc.geo.boundaryFunc );
                                 d.index=i;