From d8f1e5c76fbf3003cda173568ffc63f72d8299bc Mon Sep 17 00:00:00 2001 From: Simon Gravelle Date: Wed, 7 Feb 2024 08:40:33 +0100 Subject: [PATCH] added submodule --- .gitmodules | 3 + code/final.data | 2014 -------------------------------- code/initial.data | 2814 --------------------------------------------- code/main.py | 488 -------- code/run.ipynb | 129 --- python-codes | 1 + 6 files changed, 4 insertions(+), 5445 deletions(-) create mode 100644 .gitmodules delete mode 100644 code/final.data delete mode 100644 code/initial.data delete mode 100644 code/main.py delete mode 100644 code/run.ipynb create mode 160000 python-codes diff --git a/.gitmodules b/.gitmodules new file mode 100644 index 0000000..09e4747 --- /dev/null +++ b/.gitmodules @@ -0,0 +1,3 @@ +[submodule "python-codes"] + path = python-codes + url = git@github.com:mdcourse/python-codes.git diff --git a/code/final.data b/code/final.data deleted file mode 100644 index cfa3adc..0000000 --- a/code/final.data +++ /dev/null @@ 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-warnings.filterwarnings('ignore') - -class InitializeSimulation: - def __init__(self, - number_atoms, - Lx, - dimensions=3, - Ly = None, - Lz = None, - epsilon=0.1, - sigma=1, - atom_mass=1, - seed=None, - desired_temperature=300, - desired_pressure=1, - provided_positions=None, - provided_velocities=None, - *args, - **kwargs, - ): - super().__init__(*args, **kwargs) - self.number_atoms = number_atoms - self.Lx = Lx - self.Ly = Ly - self.Lz = Lz - self.dimensions = dimensions - self.epsilon = epsilon - self.sigma = sigma - self.atom_mass = atom_mass - self.seed = seed - self.desired_temperature = desired_temperature - self.desired_pressure = desired_pressure - self.provided_positions = provided_positions - self.provided_velocities = provided_velocities - - if self.seed is not None: - np.random.seed(self.seed) - - self.reference_distance = self.sigma - self.reference_energy = self.epsilon - self.reference_mass = self.atom_mass - self.reference_time = np.sqrt((self.reference_mass/cst.kilo/cst.Avogadro)*(self.reference_distance*cst.angstrom)**2/(self.reference_energy*cst.calorie*cst.kilo/cst.Avogadro))/cst.femto - - self.Lx = self.nondimensionalise_units(self.Lx, "distance") - self.Ly = self.nondimensionalise_units(self.Ly, "distance") - self.Lz = self.nondimensionalise_units(self.Lz, "distance") - self.epsilon = self.nondimensionalise_units(self.epsilon, "energy") - self.sigma = self.nondimensionalise_units(self.sigma, "distance") - self.atom_mass = self.nondimensionalise_units(self.atom_mass, "mass") - self.desired_temperature = self.nondimensionalise_units(self.desired_temperature, "temperature") - self.desired_pressure = self.nondimensionalise_units(self.desired_pressure, "pressure") - - self.initialize_box() - self.populate_box() - self.give_velocity() - self.write_lammps_data(filename="initial.data") - - def nondimensionalise_units(self, variable, type): - kB = cst.Boltzmann*cst.Avogadro/cst.calorie/cst.kilo # kCal/mol/K - if variable is not None: - if type == "distance": - variable /= self.reference_distance - elif type == "energy": - variable /= self.reference_energy - elif type == "mass": - variable /= self.reference_mass - elif type == "temperature": - variable /= self.reference_energy/kB - elif type == "time": - variable /= self.reference_time - elif type == "pressure": - variable *= cst.atm*cst.angstrom**3*cst.Avogadro/cst.calorie/cst.kilo/self.reference_energy*self.reference_distance**3 - else: - print("Unknown variable type", type) - return variable - - def initialize_box(self): - """Define box boundaries based on Lx, Ly, and Lz. - - If Ly or Lz or both are None, then Lx is used instead""" - box_boundaries = np.zeros((self.dimensions, 2)) - for dim, L in zip(range(self.dimensions), [self.Lx, self.Ly, self.Lz]): - if L is not None: - box_boundaries[dim] = -L/2, L/2 - else: - box_boundaries[dim] = -self.Lx/2, self.Lx/2 - box_boundaries = self.nondimensionalise_units(box_boundaries, "distance") - self.box_boundaries = box_boundaries - - def populate_box(self): - """Place atoms at random positions within the box.""" - atoms_positions = np.zeros((self.number_atoms, self.dimensions)) - if self.provided_positions is not None: - atoms_positions = self.provided_positions/self.reference_distance - else: - for dim in np.arange(self.dimensions): - atoms_positions[:, dim] = np.random.random(self.number_atoms)*np.diff(self.box_boundaries[dim]) - np.diff(self.box_boundaries[dim])/2 - self.atoms_positions = atoms_positions - - def give_velocity(self): - """Give velocity to atoms so that the initial temperature is the desired one.""" - atoms_velocities = np.zeros((self.number_atoms, self.dimensions)) - if self.provided_velocities is not None: - atoms_velocities = self.provided_velocities/self.reference_distance*self.reference_time - else: - for dim in np.arange(self.dimensions): - atoms_velocities[:, dim] = np.random.normal(size=self.number_atoms) - self.atoms_velocities = atoms_velocities - self.calculate_temperature() - scale = np.sqrt(1+((self.desired_temperature/self.temperature)-1)) - self.atoms_velocities *= scale - - -class Outputs: - def __init__(self, - thermo = None, - dump = None, - *args, - **kwargs): - self.thermo = thermo - self.dump = dump - super().__init__(*args, **kwargs) - - def evaluate_temperature(self): - """Measure temperature and convert in Kelvin.""" - # Evaluate temperature (in K) - self.calculate_temperature() - kB = cst.Boltzmann*cst.Avogadro/cst.calorie/cst.kilo # kCal/mol/K - return np.round(self.temperature*self.reference_energy/kB,2) - - def evaluate_pressure(self): - """Measure pressure and convert in atmosphere.""" - self.calculate_pressure() - return np.round(self.pressure*self.reference_energy/self.reference_distance**3*cst.calorie*cst.kilo/cst.Avogadro/cst.angstrom**3/cst.atm, 2) - - def evaluate_volume(self): - """Measure volume and convert in Angstrom 3""" - return np.round(np.prod(np.diff(self.box_boundaries))*self.reference_distance**3) - - def evaluate_potential_energy(self): - """Measure energy and convert in kcal/mol""" - Epot = self.calculate_potential_energy(self.atoms_positions) - return Epot*self.reference_energy - - def evaluate_kinetic_energy(self): - """Measure energy and convert in kcal/mol""" - self.calculate_kinetic_energy() - return self.Ekin*self.reference_energy - - def evaluate_density(self): - return self.number_atoms/np.round(np.prod(np.diff(self.box_boundaries))*self.reference_distance**3) - - def update_log(self): - if self.thermo is not None: - if (self.step % self.thermo == 0) | (self.step == 0): - temperature = self.evaluate_temperature() - pressure = self.evaluate_pressure() - volume = self.evaluate_volume() - epot = self.evaluate_potential_energy() - ekin = self.evaluate_kinetic_energy() - density = self.evaluate_density() - if self.step == 0: - print("step N temp epot ekin press vol") - print(self.step, - self.number_atoms, - temperature, - '%.2E' % Decimal(epot), - '%.2E' % Decimal(ekin), - '%.2E' % Decimal(pressure), - '%.2E' % Decimal(volume), - ) - self.write_data_file(temperature, "temperature.dat") - self.write_data_file(pressure, "pressure.dat") - self.write_data_file(volume, "volume.dat") - self.write_data_file(epot, "Epot.dat") - self.write_data_file(ekin, "Ekin.dat") - self.write_data_file(density, "density.dat") - - def write_data_file(self, output_value, filename): - if self.step == 0: - myfile = open(filename, "w") - else: - myfile = open(filename, "a") - myfile.write(str(self.step) + " " + str(output_value) + "\n") - myfile.close() - - def update_dump(self, filename="dump.lammpstrj", velocity=True): - if self.dump is not None: - if self.step % self.dump == 0: - if self.step==0: - f = open(filename, "w") - else: - f = open(filename, "a") - f.write("ITEM: TIMESTEP\n") - f.write(str(self.step) + "\n") - f.write("ITEM: NUMBER OF ATOMS\n") - f.write(str(self.number_atoms) + "\n") - f.write("ITEM: BOX BOUNDS pp pp pp\n") - for dim in np.arange(self.dimensions): - f.write(str(self.box_boundaries[dim][0]*self.reference_distance) + " " + str(self.box_boundaries[dim][1]*self.reference_distance) + "\n") - f.write("ITEM: ATOMS id type x y z vx vy vz\n") - cpt = 1 - atoms_positions = copy.deepcopy(self.atoms_positions) - if velocity: - atoms_velocities = copy.deepcopy(self.atoms_velocities) - else: - atoms_velocities = np.zeros((self.number_atoms, self.dimensions)) - for xyz, vxyz in zip(atoms_positions, atoms_velocities): - f.write(str(cpt) + " " + str(1) + " " +str(xyz[0]*self.reference_distance)+" "+str(xyz[1]*self.reference_distance)+" "+str(xyz[2]*self.reference_distance) + " " +str(vxyz[0]*self.reference_distance/self.reference_time)+" "+str(vxyz[1]*self.reference_distance/self.reference_time)+" "+str(vxyz[2]*self.reference_distance/self.reference_time)+"\n") - cpt += 1 - f.close() - - def write_lammps_data(self, filename="lammps.data"): - """Write a LAMMPS data file containing atoms positions and velocities""" - f = open(filename, "w") - f.write('# LAMMPS data file \n\n') - f.write(str(self.number_atoms)+' atoms\n') - f.write('1 atom types\n') - f.write('\n') - for LminLmax, dim in zip(self.box_boundaries*self.reference_distance, ["x", "y", "z"]): - f.write(str(LminLmax[0])+' '+str(LminLmax[1])+' '+dim+'lo ' + dim + 'hi\n') - f.write('\n') - f.write('Atoms\n') - f.write('\n') - cpt = 1 - for xyz in self.atoms_positions*self.reference_distance: - f.write(str(cpt)+ ' 1 ' + str(xyz[0]) + ' ' + str(xyz[1]) + ' ' + str(xyz[2]) +'\n') - cpt += 1 - f.write('\n') - f.write('Velocities\n') - f.write('\n') - cpt = 1 - for vxyz in self.atoms_velocities*self.reference_distance/self.reference_time: - f.write(str(cpt) + ' ' + str(vxyz[0]) + ' ' + str(vxyz[1]) + ' ' + str(vxyz[2]) +'\n') - cpt += 1 - f.close() - -class Utilities: - def __init__(self, - *args, - **kwargs): - super().__init__(*args, **kwargs) - - def calculate_kinetic_energy(self): - self.Ekin = np.sum(self.atom_mass*np.sum(self.atoms_velocities**2, axis=1)/2) - - def calculate_temperature(self): - """Follow the expression given in the LAMMPS documentation""" - self.calculate_kinetic_energy() - Ndof = self.dimensions*self.number_atoms-self.dimensions - self.temperature = 2*self.Ekin/Ndof - - def calculate_pressure(self): - """Evaluate p based on the Virial equation (Eq. 4.4.2 in Frenkel-Smith 2002)""" - Ndof = self.dimensions*self.number_atoms-self.dimensions - volume = np.prod(np.diff(self.box_boundaries)) - self.calculate_temperature() - p_ideal = (Ndof/self.dimensions)*self.temperature/volume - p_non_ideal = 1/(volume*self.dimensions)*np.sum(self.evaluate_LJ_matrix()*self.evaluate_rij_matrix()) - self.pressure = (p_ideal+p_non_ideal) - - def evaluate_rij_matrix(self): - """Evaluate vector rij between particles.""" - rij = np.zeros((self.number_atoms,self.number_atoms,3)) - for Ni in range(self.number_atoms-1): - position_i = self.atoms_positions[Ni] - for Nj in np.arange(Ni+1,self.number_atoms): - position_j = self.atoms_positions[Nj] - box_size = np.diff(self.box_boundaries).reshape(3) - rij_xyz = (np.remainder(position_i - position_j + box_size/2., box_size) - box_size/2.).T - r = np.sqrt(np.sum(rij_xyz**2)) - if r < self.cut_off: - rij[Ni][Nj] = rij_xyz - return rij - - def calculate_r(self, position_i, positions_j, number_atoms = None): - """Calculate the shortest distance between position_i and positions_j.""" - if number_atoms is None: - rij2 = np.zeros(self.number_atoms) - else: - rij2 = np.zeros(number_atoms) - box_size = np.diff(self.box_boundaries).reshape(3) - rij = (np.remainder(position_i - positions_j + box_size/2., box_size) - box_size/2.).T - for dim in np.arange(self.dimensions): - rij2 += np.power(rij[dim, :], 2) - return np.sqrt(rij2) - - def calculate_potential_energy(self, atoms_positions, number_atoms = None): - """Calculate potential energy assuming Lennard-Jones potential interaction.""" - energy_potential = 0 - for position_i in atoms_positions: - r = self.calculate_r(position_i, atoms_positions, number_atoms) - energy_potential_i = np.sum(4*(1/np.power(r[r>0], 12)-1/np.power(r[r>0], 6))) - energy_potential += energy_potential_i - energy_potential /= 2 # Avoid counting potential energy twice - return energy_potential - - def evaluate_LJ_force(self): - """Evaluate force based on LJ potential derivative.""" - forces = np.zeros((self.number_atoms,3)) - for Ni in range(self.number_atoms-1): - position_i = self.atoms_positions[Ni] - for Nj in np.arange(Ni+1,self.number_atoms): - position_j = self.atoms_positions[Nj] - box_size = np.diff(self.box_boundaries).reshape(3) - rij_xyz = (np.remainder(position_i - position_j + box_size/2., box_size) - box_size/2.).T - rij = np.sqrt(np.sum(rij_xyz**2)) - if rij < self.cut_off: - dU_dr = 48/rij*(1/rij**12-0.5/rij**6) - forces[Ni] += dU_dr*rij_xyz/rij - forces[Nj] -= dU_dr*rij_xyz/rij - return forces - - def evaluate_LJ_matrix(self): - """Evaluate force based on LJ potential derivative.""" - forces = np.zeros((self.number_atoms,self.number_atoms,3)) - for Ni in range(self.number_atoms-1): - position_i = self.atoms_positions[Ni] - for Nj in np.arange(Ni+1,self.number_atoms): - position_j = self.atoms_positions[Nj] - box_size = np.diff(self.box_boundaries).reshape(3) - rij_xyz = (np.remainder(position_i - position_j + box_size/2., box_size) - box_size/2.).T - rij = np.sqrt(np.sum(rij_xyz**2)) - if rij < self.cut_off: - dU_dr = 48/rij*(1/rij**12-0.5/rij**6) - forces[Ni][Nj] += dU_dr*rij_xyz/rij - return forces - - def wrap_in_box(self): - for dim in np.arange(self.dimensions): - out_ids = self.atoms_positions[:, dim] > self.box_boundaries[dim][1] - if np.sum(out_ids) > 0: - self.atoms_positions[:, dim][out_ids] -= np.diff(self.box_boundaries[dim])[0] - out_ids = self.atoms_positions[:, dim] < self.box_boundaries[dim][0] - if np.sum(out_ids) > 0: - self.atoms_positions[:, dim][out_ids] += np.diff(self.box_boundaries[dim])[0] - -class MolecularDynamics(InitializeSimulation, Utilities, Outputs): - def __init__(self, - maximum_steps, - tau_temp = None, - tau_press = None, - cut_off = 10, - time_step=1, - *args, - **kwargs, - ): - self.maximum_steps = maximum_steps - self.tau_temp = tau_temp - self.tau_press = tau_press - self.cut_off = cut_off - self.time_step = time_step - super().__init__(*args, **kwargs) - - self.cut_off = self.nondimensionalise_units(self.cut_off, "distance") - self.time_step = self.nondimensionalise_units(self.time_step, "time") - self.tau_temp = self.nondimensionalise_units(self.tau_temp, "time") - self.tau_press = self.nondimensionalise_units(self.tau_press, "time") - - def run(self): - """Perform the loop over time.""" - for self.step in range(0, self.maximum_steps+1): - self.integrate_equation_of_motion() - self.wrap_in_box() - if self.tau_temp is not None: - self.apply_berendsen_thermostat() - if self.tau_press is not None: - self.apply_berendsen_barostat() - self.update_log() - self.update_dump() - self.write_lammps_data(filename="final.data") - - def integrate_equation_of_motion(self): - """Integrate equation of motion using half-step velocity""" - if self.step == 0: - self.atoms_accelerations = self.evaluate_LJ_force()/self.atom_mass - atoms_velocity_Dt2 = self.atoms_velocities + self.atoms_accelerations*self.time_step/2 - self.atoms_positions = self.atoms_positions + atoms_velocity_Dt2*self.time_step - self.atoms_accelerations = self.evaluate_LJ_force()/self.atom_mass - self.atoms_velocities = atoms_velocity_Dt2 + self.atoms_accelerations*self.time_step/2 - - def apply_berendsen_thermostat(self): - """Rescale velocities based on Berendsen thermostat.""" - self.calculate_temperature() - scale = np.sqrt(1+self.time_step*((self.desired_temperature/self.temperature)-1)/self.tau_temp) - self.atoms_velocities *= scale - - def apply_berendsen_barostat(self): - """Rescale box size based on Berendsten barostat.""" - self.calculate_pressure() - scale = np.sqrt(1+self.time_step*((self.pressure/self.desired_pressure)-1)/self.tau_press) - self.box_boundaries *= scale - self.atoms_positions *= scale - - -class MonteCarlo(InitializeSimulation, Utilities, Outputs): - def __init__(self, - maximum_steps, - cut_off = 10, - displace_mc=None, - mu = None, - *args, - **kwargs, - ): - - self.maximum_steps = maximum_steps - self.cut_off = cut_off - self.displace_mc = displace_mc - self.mu = mu - super().__init__(*args, **kwargs) - - self.cut_off = self.nondimensionalise_units(self.cut_off, "distance") - self.displace_mc = self.nondimensionalise_units(self.displace_mc, "distance") - self.mu = self.nondimensionalise_units(self.mu, "energy") - - def run(self): - """Perform the loop over time.""" - - for self.step in range(0, self.maximum_steps+1): - if self.displace_mc is not None: - self.monte_carlo_displacement() - if self.mu is not None: - self.monte_carlo_insert_delete() - self.wrap_in_box() - self.update_log() - self.update_dump(velocity=False) - self.write_lammps_data(filename="final.data") - - def monte_carlo_displacement(self): - beta = 1/self.desired_temperature - Epot = self.calculate_potential_energy(self.atoms_positions) - trial_atoms_positions = copy.deepcopy(self.atoms_positions) - atom_id = np.random.randint(self.number_atoms) - trial_atoms_positions[atom_id] += (np.random.random(3)-0.5)*self.displace_mc - trial_Epot = self.calculate_potential_energy(trial_atoms_positions) - acceptation_probability = np.min([1, np.exp(-beta*(trial_Epot-Epot))]) - if np.random.random() <= acceptation_probability: - self.atoms_positions = trial_atoms_positions - self.Epot = trial_Epot - else: - self.Epot = Epot - - def calculate_Lambda(self, mass): - """Estimate de Broglie wavelength in LJ units.""" - m_kg = mass/cst.Avogadro*cst.milli*self.reference_mass - kB_kCal_mol_K = cst.Boltzmann*cst.Avogadro/cst.calorie/cst.kilo - T_K = self.desired_temperature*self.reference_energy/kB_kCal_mol_K - Lambda = cst.h/np.sqrt(2*np.pi*cst.Boltzmann*m_kg*T_K)/cst.angstrom - return self.nondimensionalise_units(Lambda, "distance") - - def monte_carlo_insert_delete(self): - Epot = self.calculate_potential_energy(self.atoms_positions) - trial_atoms_positions = copy.deepcopy(self.atoms_positions) - if np.random.random() < 0.5: - number_atoms = self.number_atoms + 1 - atom_position = np.zeros((1, self.dimensions)) - for dim in np.arange(self.dimensions): - atom_position[:, dim] = np.random.random(1)*np.diff(self.box_boundaries[dim]) - np.diff(self.box_boundaries[dim])/2 - trial_atoms_positions = np.vstack([trial_atoms_positions, atom_position]) - trial_Epot = self.calculate_potential_energy(trial_atoms_positions, number_atoms = number_atoms) - Lambda = self.calculate_Lambda(self.atom_mass) - volume = np.prod(np.diff(self.box_boundaries)) - beta = 1/self.desired_temperature - acceptation_probability = np.min([1, volume/(Lambda**self.dimensions*(self.number_atoms + 1))*np.exp(beta*(self.mu-trial_Epot+Epot))]) - else: - number_atoms = self.number_atoms - 1 - if number_atoms > 0: - atom_id = np.random.randint(self.number_atoms) - trial_atoms_positions = np.delete(trial_atoms_positions, atom_id, axis=0) - trial_Epot = self.calculate_potential_energy(trial_atoms_positions, number_atoms = number_atoms) - Lambda = self.calculate_Lambda(self.atom_mass) - volume = np.prod(np.diff(self.box_boundaries)) - beta = 1/self.desired_temperature - acceptation_probability = np.min([1, (Lambda**self.dimensions*(self.number_atoms)/volume)*np.exp(-beta*(self.mu+trial_Epot-Epot))]) - else: - acceptation_probability = 0 - if np.random.random() < acceptation_probability: - self.atoms_positions = trial_atoms_positions - self.Epot = trial_Epot - self.number_atoms = number_atoms - else: - self.Epot = Epot diff --git a/code/run.ipynb b/code/run.ipynb deleted file mode 100644 index dd819a6..0000000 --- a/code/run.ipynb +++ /dev/null @@ -1,129 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "step N temp epot ekin press vol\n", - "0 1400 nan 4.55E+05 NAN NAN 2.40E+04\n" - ] - }, - { - "ename": "KeyboardInterrupt", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[2], line 13\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mmain\u001b[39;00m \u001b[39mimport\u001b[39;00m MolecularDynamics\n\u001b[1;32m 3\u001b[0m x \u001b[39m=\u001b[39m MolecularDynamics(number_atoms\u001b[39m=\u001b[39m\u001b[39m1400\u001b[39m,\n\u001b[1;32m 4\u001b[0m Lx\u001b[39m=\u001b[39m\u001b[39m40\u001b[39m,\n\u001b[1;32m 5\u001b[0m Ly\u001b[39m=\u001b[39m\u001b[39m40\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 11\u001b[0m seed\u001b[39m=\u001b[39m\u001b[39m519817\u001b[39m,\n\u001b[1;32m 12\u001b[0m )\n\u001b[0;32m---> 13\u001b[0m x\u001b[39m.\u001b[39;49mrun()\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:369\u001b[0m, in \u001b[0;36mMolecularDynamics.run\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 367\u001b[0m \u001b[39m\u001b[39m\u001b[39m\"\"\"Perform the loop over time.\"\"\"\u001b[39;00m\n\u001b[1;32m 368\u001b[0m \u001b[39mfor\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mstep \u001b[39min\u001b[39;00m \u001b[39mrange\u001b[39m(\u001b[39m0\u001b[39m, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmaximum_steps\u001b[39m+\u001b[39m\u001b[39m1\u001b[39m):\n\u001b[0;32m--> 369\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mintegrate_equation_of_motion()\n\u001b[1;32m 370\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mwrap_in_box()\n\u001b[1;32m 371\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mtau_temp \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:385\u001b[0m, in \u001b[0;36mMolecularDynamics.integrate_equation_of_motion\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 383\u001b[0m atoms_velocity_Dt2 \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_velocities \u001b[39m+\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_accelerations\u001b[39m*\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mtime_step\u001b[39m/\u001b[39m\u001b[39m2\u001b[39m\n\u001b[1;32m 384\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_positions \u001b[39m=\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_positions \u001b[39m+\u001b[39m atoms_velocity_Dt2\u001b[39m*\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mtime_step\n\u001b[0;32m--> 385\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_accelerations \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mevaluate_LJ_force()\u001b[39m/\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39matom_mass\n\u001b[1;32m 386\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_velocities \u001b[39m=\u001b[39m atoms_velocity_Dt2 \u001b[39m+\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39matoms_accelerations\u001b[39m*\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mtime_step\u001b[39m/\u001b[39m\u001b[39m2\u001b[39m\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:313\u001b[0m, in \u001b[0;36mUtilities.evaluate_LJ_force\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 311\u001b[0m box_size \u001b[39m=\u001b[39m np\u001b[39m.\u001b[39mdiff(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mbox_boundaries)\u001b[39m.\u001b[39mreshape(\u001b[39m3\u001b[39m)\n\u001b[1;32m 312\u001b[0m rij_xyz \u001b[39m=\u001b[39m (np\u001b[39m.\u001b[39mremainder(position_i \u001b[39m-\u001b[39m position_j \u001b[39m+\u001b[39m box_size\u001b[39m/\u001b[39m\u001b[39m2.\u001b[39m, box_size) \u001b[39m-\u001b[39m box_size\u001b[39m/\u001b[39m\u001b[39m2.\u001b[39m)\u001b[39m.\u001b[39mT\n\u001b[0;32m--> 313\u001b[0m rij \u001b[39m=\u001b[39m np\u001b[39m.\u001b[39msqrt(np\u001b[39m.\u001b[39;49msum(rij_xyz\u001b[39m*\u001b[39;49m\u001b[39m*\u001b[39;49m\u001b[39m2\u001b[39;49m))\n\u001b[1;32m 314\u001b[0m \u001b[39mif\u001b[39;00m rij \u001b[39m<\u001b[39m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mcut_off:\n\u001b[1;32m 315\u001b[0m dU_dr \u001b[39m=\u001b[39m \u001b[39m48\u001b[39m\u001b[39m/\u001b[39mrij\u001b[39m*\u001b[39m(\u001b[39m1\u001b[39m\u001b[39m/\u001b[39mrij\u001b[39m*\u001b[39m\u001b[39m*\u001b[39m\u001b[39m12\u001b[39m\u001b[39m-\u001b[39m\u001b[39m0.5\u001b[39m\u001b[39m/\u001b[39mrij\u001b[39m*\u001b[39m\u001b[39m*\u001b[39m\u001b[39m6\u001b[39m)\n", - "File \u001b[0;32m<__array_function__ internals>:200\u001b[0m, in \u001b[0;36msum\u001b[0;34m(*args, **kwargs)\u001b[0m\n", - "\u001b[0;31mKeyboardInterrupt\u001b[0m: " - ] - } - ], - "source": [ - "from main import MolecularDynamics\n", - "\n", - "x = MolecularDynamics(number_atoms=1400,\n", - " Lx=40,\n", - " Ly=40,\n", - " Lz=15,\n", - " maximum_steps=100,\n", - " thermo = 10,\n", - " dump = 10, \n", - " tau_temp = 0.01,\n", - " seed=519817,\n", - " )\n", - "x.run()" - ] - }, - { - "cell_type": "code", - "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "step N temp epot ekin press vol\n", - "0 1400 300.0 4.32E+10 1.25E+03 4.94E+11 2.40E+04\n" - ] - }, - { - "ename": "KeyboardInterrupt", - "evalue": "", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[1], line 13\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[39mfrom\u001b[39;00m \u001b[39mmain\u001b[39;00m \u001b[39mimport\u001b[39;00m MonteCarlo\n\u001b[1;32m 3\u001b[0m x \u001b[39m=\u001b[39m MonteCarlo(number_atoms\u001b[39m=\u001b[39m\u001b[39m1400\u001b[39m,\n\u001b[1;32m 4\u001b[0m Lx\u001b[39m=\u001b[39m\u001b[39m40\u001b[39m,\n\u001b[1;32m 5\u001b[0m Ly\u001b[39m=\u001b[39m\u001b[39m40\u001b[39m,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 11\u001b[0m thermo \u001b[39m=\u001b[39m \u001b[39m10\u001b[39m,\n\u001b[1;32m 12\u001b[0m )\n\u001b[0;32m---> 13\u001b[0m x\u001b[39m.\u001b[39;49mrun()\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:427\u001b[0m, in \u001b[0;36mMonteCarlo.run\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 425\u001b[0m \u001b[39mfor\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mstep \u001b[39min\u001b[39;00m \u001b[39mrange\u001b[39m(\u001b[39m0\u001b[39m, \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmaximum_steps\u001b[39m+\u001b[39m\u001b[39m1\u001b[39m):\n\u001b[1;32m 426\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mdisplace_mc \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[0;32m--> 427\u001b[0m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mmonte_carlo_displacement()\n\u001b[1;32m 428\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmu \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m 429\u001b[0m \u001b[39mself\u001b[39m\u001b[39m.\u001b[39mmonte_carlo_insert_delete()\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:441\u001b[0m, in \u001b[0;36mMonteCarlo.monte_carlo_displacement\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 439\u001b[0m atom_id \u001b[39m=\u001b[39m np\u001b[39m.\u001b[39mrandom\u001b[39m.\u001b[39mrandint(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mnumber_atoms)\n\u001b[1;32m 440\u001b[0m trial_atoms_positions[atom_id] \u001b[39m+\u001b[39m\u001b[39m=\u001b[39m (np\u001b[39m.\u001b[39mrandom\u001b[39m.\u001b[39mrandom(\u001b[39m3\u001b[39m)\u001b[39m-\u001b[39m\u001b[39m0.5\u001b[39m)\u001b[39m*\u001b[39m\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mdisplace_mc\n\u001b[0;32m--> 441\u001b[0m trial_Epot \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mcalculate_potential_energy(trial_atoms_positions)\n\u001b[1;32m 442\u001b[0m acceptation_probability \u001b[39m=\u001b[39m np\u001b[39m.\u001b[39mmin([\u001b[39m1\u001b[39m, np\u001b[39m.\u001b[39mexp(\u001b[39m-\u001b[39mbeta\u001b[39m*\u001b[39m(trial_Epot\u001b[39m-\u001b[39mEpot))])\n\u001b[1;32m 443\u001b[0m \u001b[39mif\u001b[39;00m np\u001b[39m.\u001b[39mrandom\u001b[39m.\u001b[39mrandom() \u001b[39m<\u001b[39m\u001b[39m=\u001b[39m acceptation_probability:\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:298\u001b[0m, in \u001b[0;36mUtilities.calculate_potential_energy\u001b[0;34m(self, atoms_positions, number_atoms)\u001b[0m\n\u001b[1;32m 296\u001b[0m energy_potential \u001b[39m=\u001b[39m \u001b[39m0\u001b[39m\n\u001b[1;32m 297\u001b[0m \u001b[39mfor\u001b[39;00m position_i \u001b[39min\u001b[39;00m atoms_positions:\n\u001b[0;32m--> 298\u001b[0m r \u001b[39m=\u001b[39m \u001b[39mself\u001b[39;49m\u001b[39m.\u001b[39;49mcalculate_r(position_i, atoms_positions, number_atoms)\n\u001b[1;32m 299\u001b[0m energy_potential_i \u001b[39m=\u001b[39m np\u001b[39m.\u001b[39msum(\u001b[39m4\u001b[39m\u001b[39m*\u001b[39m(\u001b[39m1\u001b[39m\u001b[39m/\u001b[39mnp\u001b[39m.\u001b[39mpower(r[r\u001b[39m>\u001b[39m\u001b[39m0\u001b[39m], \u001b[39m12\u001b[39m)\u001b[39m-\u001b[39m\u001b[39m1\u001b[39m\u001b[39m/\u001b[39mnp\u001b[39m.\u001b[39mpower(r[r\u001b[39m>\u001b[39m\u001b[39m0\u001b[39m], \u001b[39m6\u001b[39m)))\n\u001b[1;32m 300\u001b[0m energy_potential \u001b[39m+\u001b[39m\u001b[39m=\u001b[39m energy_potential_i\n", - "File \u001b[0;32m~/Git/Personal/mdcourse.github.io/code/main.py:291\u001b[0m, in \u001b[0;36mUtilities.calculate_r\u001b[0;34m(self, position_i, positions_j, number_atoms)\u001b[0m\n\u001b[1;32m 289\u001b[0m rij \u001b[39m=\u001b[39m (np\u001b[39m.\u001b[39mremainder(position_i \u001b[39m-\u001b[39m positions_j \u001b[39m+\u001b[39m box_size\u001b[39m/\u001b[39m\u001b[39m2.\u001b[39m, box_size) \u001b[39m-\u001b[39m box_size\u001b[39m/\u001b[39m\u001b[39m2.\u001b[39m)\u001b[39m.\u001b[39mT\n\u001b[1;32m 290\u001b[0m \u001b[39mfor\u001b[39;00m dim \u001b[39min\u001b[39;00m np\u001b[39m.\u001b[39marange(\u001b[39mself\u001b[39m\u001b[39m.\u001b[39mdimensions):\n\u001b[0;32m--> 291\u001b[0m rij2 \u001b[39m+\u001b[39m\u001b[39m=\u001b[39m np\u001b[39m.\u001b[39;49mpower(rij[dim, :], \u001b[39m2\u001b[39;49m)\n\u001b[1;32m 292\u001b[0m \u001b[39mreturn\u001b[39;00m np\u001b[39m.\u001b[39msqrt(rij2)\n", - "\u001b[0;31mKeyboardInterrupt\u001b[0m: " - ] - } - ], - "source": [ - "from main import MonteCarlo\n", - "\n", - "x = MonteCarlo(number_atoms=1400,\n", - " Lx=40,\n", - " Ly=40,\n", - " Lz=15,\n", - " maximum_steps=5000,\n", - " displace_mc = 0.5,\n", - " seed=6987,\n", - " dump = 10,\n", - " thermo = 10,\n", - " )\n", - "x.run()" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 3", - "language": "python", - "name": "python3" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 3 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython3", - "version": "3.10.7" - } - }, - "nbformat": 4, - "nbformat_minor": 4 -} diff --git a/python-codes b/python-codes new file mode 160000 index 0000000..7b63e85 --- /dev/null +++ b/python-codes @@ -0,0 +1 @@ +Subproject commit 7b63e859d9207877e1a8a91bfc82bbd576f45690