Merge pull request #1965 from glotzerlab/fix-nec

Fix NEC integrators
glotzerlab · Dec 5, 2024 · 58b7ba5 · 58b7ba5
2 parents ab1ba91 + 661d39e
commit 58b7ba5
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Showing 6 changed files with 67 additions and 38 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -4,6 +4,15 @@ Change Log
 5.x
 ---
 
+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)
 ^^^^^^^^^^^^^^^^^^
 

diff --git a/hoomd/hpmc/IntegratorHPMCMonoNEC.h b/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++)

diff --git a/hoomd/hpmc/compute.py b/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

diff --git a/hoomd/hpmc/nec/integrate.py b/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(

diff --git a/hoomd/hpmc/pytest/CMakeLists.txt b/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

diff --git a/hoomd/hpmc/pytest/test_nec.py b/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)