Merge pull request #72 from maximillian-dolan/master

adjusting docstrings

pylj/forcefields.py

@@ -27,7 +27,7 @@ def energy(self, dr):
         .. math::
             E = \frac{4e*a^{12}}{dr^{12}} - \frac{4e*a^{6}}{dr^6}
 
-        Attributes:
+        Parameters
         ----------
         dr (float): The distance between particles.
  
@@ -47,7 +47,7 @@ def force(self, dr):
         .. math::
             f = \frac{48e*a^{12}}{dr^{13}} - \frac{24e*a^{6}}{dr^7}
 
-        Attributes:
+        Parameters
         ----------
         dr (float): The distance between particles.
  
@@ -110,7 +110,7 @@ def mixing(self, constants_2):
             a = 4*\epsilon*(\sigma^12)
             b = 4*\epsilon*(\sigma^6)
 
-        Parameters:
+        Parameters
         ----------
         constants_2: float, array_like
             The second set of constantss
@@ -150,7 +150,7 @@ def energy(self, dr):
         .. math::
             E = Ae^{(-Bdr)} - \frac{C}{dr^6}
 
-        Attributes:
+        Parameters
         ----------
         dr (float): The distance between particles.
  
@@ -175,7 +175,7 @@ def force(self, dr):
         .. math::
             f = ABe^{(-Bdr)} - \frac{6C}{dr^7}
 
-        Attributes:
+        Parameters
         ----------
         dr (float): The distance between particles.
  
@@ -201,7 +201,7 @@ def mixing(self, constants2):
             b_{12} = \sqrt{b_1 * b_2}
             c_{12} = \sqrt{c_1 * c_2}
         
-        Attributes:
+        Parameters
         ----------
         constants_2: float, array_like
             The second set of constantss
@@ -247,7 +247,7 @@ def energy(self, dr):
                 E = 0
             }
 
-        Attributes:
+        Parameters
         ----------
         dr (float): The distance between particles.
  

pylj/md.py

@@ -84,6 +84,7 @@ def velocity_verlet(
     Updates the particles positions and velocities in terms of the Velocity
     Verlet algorithm. Also calculates the instanteous temperature, pressure,
     and force and appends these to the appropriate system array.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -92,6 +93,7 @@ def velocity_verlet(
         Length for each Velocity-Verlet integration step, in seconds.
     box_length: float
         Length of a single dimension of the simulation square, in Angstrom.
+
     Returns
     -------
     util.particle_dt, array_like:
@@ -127,6 +129,7 @@ def velocity_verlet(
 
 def sample(particles, box_length, initial_particles, system):
     """Sample parameters of interest in the simulation.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -137,6 +140,7 @@ def sample(particles, box_length, initial_particles, system):
         Information about the initial particle conformation.
     system: System
         Details about the whole system
+
     Returns
     -------
     System:
@@ -165,6 +169,7 @@ def sample(particles, box_length, initial_particles, system):
 
 def calculate_msd(particles, initial_particles, box_length):
     """Determines the mean squared displacement of the particles in the system.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -173,6 +178,7 @@ def calculate_msd(particles, initial_particles, box_length):
         Information about the initial state of the particles.
     box_length: float
         Size of the cell vector.
+
     Returns
     -------
     float:
@@ -205,6 +211,7 @@ def update_positions(
     positions, old_positions, velocities, accelerations, timestep_length, box_length
 ):
     """Update the particle positions using the Velocity-Verlet integrator.
+
     Parameters
     ----------
     positions: (2, N) array_like
@@ -224,6 +231,7 @@ def update_positions(
         Length for each Velocity-Verlet integration step, in seconds.
     box_length: float
         Length of a single dimension of the simulation square, in Angstrom.
+
     Returns
     -------
     (2, N) array_like:
@@ -246,6 +254,7 @@ def update_velocities(
     velocities, accelerations_old, accelerations_new, timestep_length
 ):
     """Update the particle velocities using the Velocity-Verlet algoritm.
+
     Parameters
     ----------
     velocities: (2, N) array_like
@@ -257,6 +266,7 @@ def update_velocities(
         accelerations.
     timestep_length: float
         Length for each Velocity-Verlet integration step, in seconds.
+
     Returns
     -------
     (2, N) array_like:
@@ -273,10 +283,12 @@ def update_velocities(
 
 def calculate_temperature(particles, mass):
     """Determine the instantaneous temperature of the system.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
         Information about the particles.
+
     Returns
     -------
     float:
@@ -297,6 +309,7 @@ def calculate_temperature(particles, mass):
 def compute_force(particles, box_length, cut_off, constants, forcefield, mass):
     r"""Calculates the forces and therefore the accelerations on each of the
     particles in the simulation.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -313,6 +326,7 @@ def compute_force(particles, box_length, cut_off, constants, forcefield, mass):
         The particular forcefield to be used to find the energy and forces.
     mass: float (optional)
         The mass of the particle being simulated (units of atomic mass units).
+
     Returns
     -------
     util.particle_dt, array_like
@@ -337,6 +351,7 @@ def heat_bath(particles, temperature_sample, bath_temperature):
     .. math::
         v_{\text{new}} = v_{\text{old}} \times
         \sqrt{\frac{T_{\text{desired}}}{\bar{T}}}
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -345,6 +360,7 @@ def heat_bath(particles, temperature_sample, bath_temperature):
         The temperature at each timestep in the simulation.
     bath_temp: float
         The desired temperature of the simulation.
+        
     Returns
     -------
     util.particle_dt, array_like

pylj/pairwise.py

@@ -6,6 +6,7 @@
 def compute_force(particles, box_length, cut_off, constants, forcefield, mass):
     r"""Calculates the forces and therefore the accelerations on each of the
     particles in the simulation.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -22,6 +23,7 @@ def compute_force(particles, box_length, cut_off, constants, forcefield, mass):
         The particular forcefield to be used to find the energy and forces.
     mass: float (optional)
         The mass of the particle being simulated (units of atomic mass units).
+
     Returns
     -------
     util.particle_dt, array_like
@@ -73,6 +75,7 @@ def compute_force(particles, box_length, cut_off, constants, forcefield, mass):
 #Jit tag here had to be removed
 def separation(dx, dy):
     """Calculate the distance in 2D space.
+
     Parameters
     ----------
     dx: float
@@ -88,6 +91,7 @@ def separation(dx, dy):
 
 def update_accelerations(particles, f, m, dx, dy, dr):
     """Update the acceleration arrays of particles.
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -124,6 +128,7 @@ def update_accelerations(particles, f, m, dx, dy, dr):
 def second_law(f, m, d1, d2):
     """Newton's second law of motion to get the acceleration of the particle
     in a given dimension.
+
     Parameters
     ----------
     f: float
@@ -204,6 +209,7 @@ def calculate_pressure(
     .. math::
         p = \langle \rho k_b T \rangle + \bigg\langle \frac{1}{3V}\sum_{i}
         \sum_{j<i} \mathbf{r}_{ij}\mathbf{f}_{ij} \bigg\rangle
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -222,6 +228,7 @@ def calculate_pressure(
         The particular forcefield to be used to find the energy and forces.
     mass: float (optional)
         The mass of the particle being simulated (units of atomic mass units).
+
     Returns
     -------
     float:
@@ -248,6 +255,7 @@ def heat_bath(particles, temperature_sample, bath_temp):
     .. math::
         v_{\text{new}} = v_{\text{old}} \times
         \sqrt{\frac{T_{\text{desired}}}{\bar{T}}}
+
     Parameters
     ----------
     particles: util.particle_dt, array_like
@@ -256,6 +264,7 @@ def heat_bath(particles, temperature_sample, bath_temp):
         The temperature at each timestep in the simulation.
     bath_temp: float
         The desired temperature of the simulation.
+
     Returns
     -------
     util.particle_dt, array_like
@@ -270,6 +279,7 @@ def heat_bath(particles, temperature_sample, bath_temp):
 #Jit tag here had to be removed
 def dist(xposition, yposition, box_length, types):
     """Returns the distance array for the set of particles.
+
     Parameters
     ----------
     xpos: float, array_like (N)
@@ -283,6 +293,7 @@ def dist(xposition, yposition, box_length, types):
     types: str, array_like (N)
         Array of length N, where N is the number of particles, providing the
         type of each particle.
+
     Returns
     -------
     drr: float, array_like ((N - 1) * N / 2))
@@ -318,12 +329,14 @@ def dist(xposition, yposition, box_length, types):
 #Jit tag here had to be removed
 def pbc_correction(position, cell):
     """Correct for the periodic boundary condition.
+
     Parameters
     ----------
     position: float
         Particle position.
     cell: float
         Cell vector.
+
     Returns
     -------
     float:
@@ -336,11 +349,13 @@ def create_dist_identifiers(type_identifier):
     '''
     Creates correct distance identifier matrix for particular type
     of particle
+
     Parameters
-    -------
+    ----------
     type identifiers:
         the identifier array listing 1 for particles of that type
         or 0 for particles of a different type
+
     Returns
     -------
     distances: float, array_like 

pylj/util.py

@@ -10,6 +10,7 @@ class System:
     is being run. This includes the particles
     object, as will as sampling objects such as the temperature, pressure, etc.
     arrays.
+
     Parameters
     ----------
     number_of_particles: int
@@ -310,6 +311,7 @@ def __version__():  # pragma: no cover
 
 def particle_dt():
     """Builds the data type for the particles, this consists of:
+    
     - xposition and yposition
     - xvelocity and yvelocity
     - xacceleration and yacceleration