Merge remote-tracking branch 'origin' into joss-paper

README.md

@@ -4,15 +4,25 @@ This code allows you to launch Metropolis Monte Carlo simulations via Heisenberg
 
 ## How to compile
 
-Download all files and run `python setup.py build_ext --inplace`.
+`mamonca` can be installed directly from conda:
+
+```
+conda install -c conda-forge mamonca
+```
+In order to use build it from the repository, run
+```
+git clone https://github.com/samwaseda/mamonca
+cd mamonca
+python setup.py build_ext --user
+```
 
 ## First steps:
 
 In the following simple (but complete) example, we create a bcc Fe system using [pyiron](http://github.com/pyiron/pyiron) and launch a Metropolis Monte Carlo simulation with a Heisenberg coefficient `J=0.1` (eV) for the first nearest neighbor pairs:
 
 ```python
-from pyiron import Project
-from mc import MC
+from pyiron_atomistics import Project
+from mamonca import MC
 
 structure = Project('.').create.structure.bulk(
     name='Fe',

tests/test_full_run.py

@@ -0,0 +1,47 @@
+from mamonca import MC
+import numpy as np
+import unittest
+import os
+
+
+class TestTemplate(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        cls.file_location = os.path.dirname(os.path.abspath(__file__))
+        cls.ij = np.loadtxt(
+            os.path.join(cls.file_location, "neighbors.txt")
+        ).astype(int)
+        cls.n = np.max(cls.ij) + 1
+
+
+class TestRaw(TestTemplate):
+
+    def test_thermodynamic_integration(self):
+        mc = MC(self.n)
+        mc.set_heisenberg_coeff(0.1, *self.ij, index=0)
+        mc.set_heisenberg_coeff(-0.03, *self.ij, index=1)
+        mc.set_lambda(0.5)
+        mc.run(temperature=300, number_of_iterations=100)
+        self.assertLess(mc.get_energy(index=0), mc.get_energy(index=1))
+
+class TestPredefine(TestTemplate):
+    def setUp(self):
+        self.mc = MC(self.n)
+        self.mc.set_heisenberg_coeff(0.1, *self.ij, index=0)
+
+    def test_metadynamics(self):
+        self.mc.set_metadynamics(max_range=1)
+        self.mc.run(temperature=300, number_of_iterations=100)
+        meta = self.mc.get_metadynamics_free_energy()
+        self.assertAlmostEqual(np.diff(meta["magnetization"]).ptp(), 0)
+        self.assertLessEqual(meta["free_energy"].max(), 0)
+
+    def test_spin_dynamics(self):
+        self.mc.switch_spin_dynamics()
+        self.mc.run(temperature=300, number_of_iterations=100)
+        self.assertLess(self.mc.get_energy(), 0)
+
+
+if __name__ == '__main__':
+    unittest.main()