Merge pull request #28 from arm61/2.0

1.1

appveyor.yml

@@ -39,16 +39,16 @@ test_script:
   # to put the Python version you want to use on PATH.
   - "python setup.py test"
 
-after_test:
+#after_test:
   # This step builds your wheels.
   # Again, you only need build.cmd if you're building C extensions for
   # 64-bit Python 3.3/3.4. And you need to use %PYTHON% to get the correct
   # interpreter
-  - "python setup.py bdist_wheel"
+  #- "python setup.py bdist_wheel"
 
-artifacts:
+#artifacts:
   # bdist_wheel puts your built wheel in the dist directory
-  - path: dist\*
+  #- path: dist\*
 
 #on_success:
 #  You can use this step to upload your artifacts to a public website.

pylj/forcefields.py

@@ -0,0 +1,27 @@
+import numpy as np
+
+
+def lennard_jones(dr, constants, force=False):
+    """Calculate the energy of a pair of particles at a given distance.
+
+    Parameters
+    ----------
+    dr: float, array_like
+        The distances between the all pairs of particles.
+    constants: float, array_like
+        An array of lenght two consisting of the A and B parameters for the
+        12-6 Lennard-Jones function.
+    force: bool (optional)
+        If true, the negative first derivative will be found.
+
+    Returns
+    -------
+    float:
+        The potential energy or force between the particles.
+    """
+    if force:
+        return 12 * constants[0] * np.power(dr, -13) - (6 * constants[1] *
+                                                        np.power(dr, -7))
+    else:
+        return constants[0] * np.power(dr, -12) - (constants[1] *
+                                                   np.power(dr, -6))

pylj/md.py

@@ -1,9 +1,6 @@
 import numpy as np
-try:
-    from pylj import comp as heavy
-except ImportError:
-    print("WARNING, using slow force and energy calculations")
-    from pylj import pairwise as heavy
+from pylj import pairwise as heavy
+from pylj import forcefields as ff
 
 
 def initialise(number_of_particles, temperature, box_length, init_conf,
@@ -88,9 +85,9 @@ def velocity_verlet(particles, timestep_length, box_length, cut_off):
     [particles['xprevious_position'], particles['yprevious_position']] = pos
     xacceleration_store = list(particles['xacceleration'])
     yacceleration_store = list(particles['yacceleration'])
-    particles, distances, forces, energies = heavy.compute_forces(particles,
-                                                                  box_length,
-                                                                  cut_off)
+    particles, distances, forces, energies = heavy.compute_force(particles,
+                                                                 box_length,
+                                                                 cut_off)
     [particles['xvelocity'], particles['yvelocity']] = update_velocities(
         [particles['xvelocity'], particles['yvelocity']],
         [xacceleration_store, yacceleration_store],
@@ -126,7 +123,8 @@ def sample(particles, box_length, initial_particles, system):
     system.temperature_sample = np.append(system.temperature_sample,
                                           temperature_new)
     pressure_new = heavy.calculate_pressure(particles, box_length,
-                                            temperature_new, system.cut_off)
+                                            temperature_new, system.cut_off,
+                                            system.constants)
     msd_new = calculate_msd(particles, initial_particles, box_length)
     system.pressure_sample = np.append(system.pressure_sample, pressure_new)
     system.force_sample = np.append(system.force_sample,
@@ -272,3 +270,29 @@ def calculate_temperature(particles):
         k += mass_of_argon * v * v / (boltzmann_constant * 2 *
                                       particles['xposition'].size)
     return k
+
+
+def compute_force(particles, box_length, cut_off,
+                  constants=[1.363e-134, 9.273e-78], mass=39.948,
+                  forcefield=ff.lennard_jones):
+    part, dist, forces, energies = heavy.compute_force(particles, box_length,
+                                                       cut_off,
+                                                       constants=constants,
+                                                       mass=mass,
+                                                       forcefield=forcefield)
+    return part, dist, forces, energies
+
+
+def compute_energy(particles, box_length, cut_off,
+                   constants=[1.363e-134, 9.273e-78],
+                   forcefield=ff.lennard_jones):
+    dist, energies = heavy.compute_energy(particles, box_length, cut_off,
+                                          constants=constants,
+                                          forcefield=forcefield)
+    return dist, energies
+
+
+def heat_bath(particles, temperature_sample, bath_temperature):
+    particles = heavy.heat_bath(particles, temperature_sample,
+                                bath_temperature)
+    return particles