Add force support for HarmonicTorsion

cmake/ExternalTools.cmake

@@ -204,8 +204,8 @@ endif()
 
 FetchContent_Declare(
     eigen
-    URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz"
-    URL_HASH MD5=9e30f67e8531477de4117506fe44669b)
+    URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz"
+    URL_HASH MD5=609286804b0f79be622ccf7f9ff2b660)
 FetchContent_GetProperties(eigen)
 if(NOT eigen_POPULATED)
     FetchContent_Populate(eigen)

examples/CMakeLists.txt

@@ -69,6 +69,14 @@ add_test(
     && ${PYTHON_EXECUTABLE} ${JSON_COMPARE} minimal.out.json out.json --tol 0.02"
         WORKING_DIRECTORY ${EXAMPLES_DIR}/minimal)
 
+add_test(
+        NAME bend
+        COMMAND sh -c "${PYTHON_EXECUTABLE} ${YASON} bend.yml\
+    | $<TARGET_FILE:faunus> --nobar\
+    && ${PYTHON_EXECUTABLE} ${JSON_COMPARE} bend.out.json out.json --tol 0.03"
+        WORKING_DIRECTORY ${EXAMPLES_DIR}/bend)
+
+
 add_test(
         NAME chain
         COMMAND sh -c "${PYTHON_EXECUTABLE} ${YASON} chain.yml\
@@ -236,6 +244,9 @@ install(FILES
         ${EXAMPLES_DIR}/minimal/minimal.yml
         ${EXAMPLES_DIR}/minimal/minimal.out.json
         ${EXAMPLES_DIR}/minimal/minimal.state.json
+        ${EXAMPLES_DIR}/bend/bend.yml
+        ${EXAMPLES_DIR}/bend/bend.out.json
+        ${EXAMPLES_DIR}/bend/mc_vs_md.agr
         ${EXAMPLES_DIR}/penalty/penalty.yml
         ${EXAMPLES_DIR}/penalty/penalty.ipynb
         ${EXAMPLES_DIR}/multipole/multipole.yml

examples/bend/bend.out.json

@@ -0,0 +1,162 @@
+{
+  "analysis": [
+    {
+      "systemenergy": {
+        "file": "energy.dat",
+        "final": [
+          1.773122609062241
+        ],
+        "init": 1.4933,
+        "nskip": 1,
+        "nstep": 100,
+        "samples": 2000
+      }
+    },
+    {
+      "reactioncoordinate": {
+        "average": 1.990380828288927,
+        "dir": [
+          1.0,
+          1.0,
+          1.0
+        ],
+        "file": "distance.dat.gz",
+        "index": 0,
+        "indexes": [
+          0,
+          2
+        ],
+        "nskip": 10,
+        "nstep": 1,
+        "property": "atomatom",
+        "samples": 199990,
+        "type": "molecule"
+      }
+    },
+    {
+      "atomrdf": {
+        "dim": 1,
+        "dr": 0.1,
+        "file": "rdf.dat",
+        "name1": "bead",
+        "name2": "bead",
+        "nskip": 1,
+        "nstep": 1,
+        "samples": 199999,
+        "slicedir": [
+          0,
+          0,
+          0
+        ],
+        "thickness": 0.0
+      }
+    }
+  ],
+  "compiler": "10.2.1 20201220",
+  "energy": [
+    {
+      "hamiltonian": [
+        {
+          "bonded": {
+            "bondlist-intramolecular": [
+              {
+                "harmonic": {
+                  "index": [
+                    0,
+                    1
+                  ],
+                  "k": 10.0,
+                  "req": 1.0
+                }
+              },
+              {
+                "harmonic": {
+                  "index": [
+                    1,
+                    2
+                  ],
+                  "k": 10.0,
+                  "req": 1.0
+                }
+              },
+              {
+                "harmonic_torsion": {
+                  "aeq": 90.0,
+                  "index": [
+                    0,
+                    1,
+                    2
+                  ],
+                  "k": 10.0
+                }
+              }
+            ],
+            "relative time": 0.05504322236267151
+          }
+        }
+      ]
+    }
+  ],
+  "geometry": {
+    "length": [
+      20.0,
+      20.0,
+      20.0
+    ],
+    "type": "cuboid"
+  },
+  "git revision": "d3ce821d (2021-05-04)",
+  "groups": [
+    {
+      "threebody": {
+        "compressible": false,
+        "index": [
+          0,
+          2
+        ],
+        "size": 3
+      }
+    }
+  ],
+  "montecarlo": {
+    "average potential energy (kT)": 1.796037325037313,
+    "last move": "langevin_dynamics"
+  },
+  "moves": [
+    {
+      "langevin_dynamics": {
+        "acceptance": 1.0,
+        "integrator": {
+          "friction": 5.0,
+          "time_step": 0.005
+        },
+        "moves": 200259,
+        "nsteps": 10,
+        "relative time": 0.713,
+        "relative time (without energy calc)": 0.663,
+        "repeat": 1
+      }
+    },
+    {
+      "transrot": {
+        "acceptance": 0.21,
+        "dir": [
+          1.0,
+          1.0,
+          1.0
+        ],
+        "molecule": "threebody",
+        "molid": 0,
+        "moves": 599741,
+        "relative time": 0.236,
+        "relative time (without energy calc)": 0.108,
+        "repeat": 3,
+        "√⟨r²⟩": 0.539
+      }
+    }
+  ],
+  "number of groups": 1,
+  "number of particles": 3,
+  "reactionlist": null,
+  "temperature": 298.15
+}

examples/bend/bend.yml

@@ -0,0 +1,57 @@
+#!/usr/bin/env yason.py
+#
+# Combined MC and MD moves on a three-bead molecule
+# with two harmonic bonds and a harmonic bond angle
+#
+# You may disable either MD or MC to verify that they
+# individually give the same bead<->bead distribution
+#
+energy:
+    - bonded: {}
+
+atomlist:
+    - middle_bead: {mw: 1, dp: 5}
+    - bead: {mw: 1, dp: 5}
+
+moleculelist:
+    - threebody:
+        atomic: false
+        atoms: [bead, middle_bead, bead]
+        structure:
+          - bead: [-1.14, -4.98, 8.99]
+          - middle_bead: [0.039, -6.39, 9.10]
+          - bead: [-0.82, -7.13, 9.42]
+        bondlist:
+          - harmonic: {k: 10, req: 1, index: [0,1]}
+          - harmonic: {k: 10, req: 1, index: [1,2]}
+          - harmonic_torsion: {k: 10, aeq: 90, index: [0,1,2]}
+
+insertmolecules:
+    - threebody: {N: 1}
+
+moves:
+    - langevin_dynamics: # Langevin dynamics
+        nsteps: 10
+        integrator: {time_step: 0.005, friction: 5}
+    - transrot: # Monte Carlo
+        molecule: threebody
+
+analysis:
+    - systemenergy: {file: energy.dat, nstep: 100, nskip: 1}
+    - reactioncoordinate:
+          file: distance.dat.gz
+          nstep: 1
+          nskip: 10
+          type: molecule
+          index: 0
+          property: atomatom
+          indexes: [0,2]
+          dir: [1,1,1]
+    - atomrdf: {file: rdf.dat, nstep: 1, dr: 0.1, name1: bead, name2: bead, nskip: 1, dim: 1}
+    - savestate: {file: state.json}
+
+geometry: {type: cuboid, length: 20}
+mcloop: {macro: 1, micro: 200000}
+temperature: 298.15
+random: { seed: fixed }
+