Wang frenkel

.github/workflows/build_and_test.yaml

@@ -122,7 +122,7 @@ jobs:
         submodules: true
 
     - name: Create Python Environment
-      uses: mamba-org/setup-micromamba@617811f69075e3fd3ae68ca64220ad065877f246 # v2.0.0
+      uses: mamba-org/setup-micromamba@06375d89d211a1232ef63355742e9e2e564bc7f7 # v2.0.2
       with:
         micromamba-version: '2.0.2-2'
         environment-name: test
@@ -219,7 +219,7 @@ jobs:
         path: code
 
     - name: Create Python Environment
-      uses: mamba-org/setup-micromamba@617811f69075e3fd3ae68ca64220ad065877f246 # v2.0.0
+      uses: mamba-org/setup-micromamba@06375d89d211a1232ef63355742e9e2e564bc7f7 # v2.0.2
       with:
         micromamba-version: '2.0.2-2'
         environment-name: test

.github/workflows/release.yaml

@@ -86,7 +86,7 @@ jobs:
         name: release
 
     - name: Create release
-      uses: softprops/action-gh-release@e7a8f85e1c67a31e6ed99a94b41bd0b71bbee6b8 # v2.0.9
+      uses: softprops/action-gh-release@01570a1f39cb168c169c802c3bceb9e93fb10974 # v2.1.0
       if: startsWith(github.ref, 'refs/tags/v')
       with:
         files: "*.tar.*"

CHANGELOG.rst

@@ -4,6 +4,18 @@ Change Log
 5.x
 ---
 
+*Added*
+* Wang-Frenkel potential
+
+5.0.1 (not yet released)
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+*Fixed*
+
+* Prevent ``missing 1 required positional argument: 'kT'`` errors when using NEC integrators
+  (`#1965 <https://github.com/glotzerlab/hoomd-blue/pull/1965>`__)
+
+
 5.0.0 (2024-12-02)
 ^^^^^^^^^^^^^^^^^^
 

hoomd/HOOMDMath.h

@@ -349,6 +349,50 @@ inline HOSTDEVICE double pow(double x, double y)
     return ::exp(y * log(x));
     }
 
+//! Compute the pow of x,y in double precision when y is an integer using squaring
+inline HOSTDEVICE double pow(double x, unsigned int y){
+        double result = 1.0;
+        for(;;){
+                if(y & 1)
+                    result *= x;
+                y >>= 1;
+                if(!y)
+                    break;
+                x *= x;
+            }
+        return result;
+    }
+
+inline HOSTDEVICE double pow(double x, int y){
+    unsigned int _y = abs(y);
+    if(y < 0)
+        return 1.0 / pow(x, _y);
+    else
+        return pow(x,_y);
+    }
+
+//! Compute the pow of x,y in single precision when y is an integer using squaring
+inline HOSTDEVICE float pow(float x, unsigned int y){
+    float result = 1.0f;
+    for(;;){
+        if(y & 1)
+            result *= x;
+        y >>= 1;
+        if(!y)
+            break;
+        x *= x;
+        }
+    return result;
+    }
+
+inline HOSTDEVICE float pow(float x, int y){
+    unsigned int _y = abs(y);
+    if(y < 0)
+        return 1.0f / pow(x, _y);
+    else
+        return pow(x,_y);
+    }
+
 //! Compute the exp of x
 inline HOSTDEVICE float exp(float x)
     {

hoomd/hpmc/IntegratorHPMCMonoNEC.h

@@ -275,17 +275,12 @@ template<class Shape> void IntegratorHPMCMonoNEC<Shape>::update(uint64_t timeste
     this->m_exec_conf->msg->notice(10) << "HPMCMonoEC update: " << timestep << std::endl;
     IntegratorHPMC::update(timestep);
 
-    // get needed vars
-    ArrayHandle<hpmc_counters_t> h_counters(this->m_count_total,
-                                            access_location::host,
-                                            access_mode::readwrite);
-    hpmc_counters_t& counters = h_counters.data[0];
-
-    ArrayHandle<hpmc_nec_counters_t> h_nec_counters(m_nec_count_total,
-                                                    access_location::host,
-                                                    access_mode::readwrite);
-    hpmc_nec_counters_t& nec_counters = h_nec_counters.data[0];
-    m_nec_count_step_start = h_nec_counters.data[0];
+        {
+        ArrayHandle<hpmc_nec_counters_t> h_nec_counters(m_nec_count_total,
+                                                        access_location::host,
+                                                        access_mode::readwrite);
+        m_nec_count_step_start = h_nec_counters.data[0];
+        }
 
     const BoxDim& box = this->m_pdata->getBox();
     unsigned int ndim = this->m_sysdef->getNDimensions();
@@ -294,29 +289,6 @@ template<class Shape> void IntegratorHPMCMonoNEC<Shape>::update(uint64_t timeste
     count_pressurevirial = 0.0;
     count_movelength = 0.0;
 
-    // access interaction matrix
-    ArrayHandle<unsigned int> h_overlaps(this->m_overlaps,
-                                         access_location::host,
-                                         access_mode::read);
-    ArrayHandle<int3> h_image(this->m_pdata->getImages(),
-                              access_location::host,
-                              access_mode::readwrite);
-
-    // access particle data
-    ArrayHandle<Scalar4> h_postype(this->m_pdata->getPositions(),
-                                   access_location::host,
-                                   access_mode::readwrite);
-    ArrayHandle<Scalar4> h_velocities(this->m_pdata->getVelocities(),
-                                      access_location::host,
-                                      access_mode::readwrite);
-    ArrayHandle<Scalar4> h_orientation(this->m_pdata->getOrientationArray(),
-                                       access_location::host,
-                                       access_mode::readwrite);
-
-    // access move sizes
-    ArrayHandle<Scalar> h_d(this->m_d, access_location::host, access_mode::read);
-    ArrayHandle<Scalar> h_a(this->m_a, access_location::host, access_mode::read);
-
     uint16_t seed = this->m_sysdef->getSeed();
 
     // loop over local particles nselect times
@@ -333,6 +305,40 @@ template<class Shape> void IntegratorHPMCMonoNEC<Shape>::update(uint64_t timeste
         // update the image list
         this->updateImageList();
 
+        // get needed vars
+        ArrayHandle<hpmc_counters_t> h_counters(this->m_count_total,
+                                                access_location::host,
+                                                access_mode::readwrite);
+        hpmc_counters_t& counters = h_counters.data[0];
+
+        ArrayHandle<hpmc_nec_counters_t> h_nec_counters(m_nec_count_total,
+                                                        access_location::host,
+                                                        access_mode::readwrite);
+        hpmc_nec_counters_t& nec_counters = h_nec_counters.data[0];
+
+        // access interaction matrix
+        ArrayHandle<unsigned int> h_overlaps(this->m_overlaps,
+                                             access_location::host,
+                                             access_mode::read);
+        ArrayHandle<int3> h_image(this->m_pdata->getImages(),
+                                  access_location::host,
+                                  access_mode::readwrite);
+
+        // access particle data
+        ArrayHandle<Scalar4> h_postype(this->m_pdata->getPositions(),
+                                       access_location::host,
+                                       access_mode::readwrite);
+        ArrayHandle<Scalar4> h_velocities(this->m_pdata->getVelocities(),
+                                          access_location::host,
+                                          access_mode::readwrite);
+        ArrayHandle<Scalar4> h_orientation(this->m_pdata->getOrientationArray(),
+                                           access_location::host,
+                                           access_mode::readwrite);
+
+        // access move sizes
+        ArrayHandle<Scalar> h_d(this->m_d, access_location::host, access_mode::read);
+        ArrayHandle<Scalar> h_a(this->m_a, access_location::host, access_mode::read);
+
         // loop through N particles in a shuffled order
         for (unsigned int cur_chain = 0; cur_chain < this->m_pdata->getN() * m_update_fraction;
              cur_chain++)

hoomd/hpmc/compute.py

@@ -7,8 +7,6 @@
 particles and `SDF` samples the pressure.
 """
 
-from __future__ import print_function
-
 from hoomd import _hoomd
 from hoomd.operation import Compute
 from hoomd.hpmc import _hpmc

hoomd/hpmc/nec/integrate.py

@@ -72,7 +72,7 @@ def __init__(
         nselect=1,
     ):
         # initialize base class
-        super().__init__(default_d, default_a, 0.5, nselect)
+        super().__init__(default_d, default_a, 0.5, nselect, 1.0)
 
         # Set base parameter dict for hpmc chain integrators
         param_dict = ParameterDict(

hoomd/hpmc/pytest/CMakeLists.txt

@@ -13,9 +13,10 @@ set(files __init__.py
           test_shape_updater.py
           test_shape_utils.py
           test_move_size_tuner.py
+          test_nec.py
           test_pair_lennard_jones.py
           test_pair_expanded_gaussian.py
-	      test_pair_lj_gauss.py
+          test_pair_lj_gauss.py
           test_pair_opp.py
           test_pair_step.py
           test_pair_union.py

hoomd/hpmc/pytest/test_nec.py

@@ -0,0 +1,15 @@
+# Copyright (c) 2009-2024 The Regents of the University of Michigan.
+# Part of HOOMD-blue, released under the BSD 3-Clause License.
+
+import hoomd
+import pytest
+
+
+@pytest.mark.serial
+def test_nec(simulation_factory, lattice_snapshot_factory):
+    snap = lattice_snapshot_factory(particle_types=["A"])
+    simulation = simulation_factory(snap)
+    sphere = hoomd.hpmc.nec.integrate.Sphere()
+    sphere.shape["A"] = {"diameter": 1.0}
+    simulation.operations.integrator = sphere
+    simulation.run(10)

hoomd/md/CMakeLists.txt

@@ -126,6 +126,7 @@ set(_md_headers ActiveForceComputeGPU.h
                 EvaluatorPairTable.h
                 EvaluatorPairTWF.h
                 EvaluatorPairYukawa.h
+                EvaluatorPairWangFrenkel.h
                 EvaluatorPairZBL.h
                 EvaluatorTersoff.h
                 EvaluatorWalls.h
@@ -556,7 +557,8 @@ set(_pair_evaluators Buckingham
                      LJGauss
                      ForceShiftedLJ
                      Table
-                     ExpandedGaussian)
+                     ExpandedGaussian
+                     WangFrenkel)
 
 
 foreach(_evaluator ${_pair_evaluators})