From 02577fe4b38ffd48b29399aed37a8644dd2cd6ca Mon Sep 17 00:00:00 2001 From: Jenny <39961845+jennyfothergill@users.noreply.github.com> Date: Thu, 20 Jul 2023 16:04:55 -0600 Subject: [PATCH] Add rigid pentane model for hoomd (#181) * Fix molecule check for exclusions * Add logic for constrained bonds for pentaneUA * Add print for rigid and constrained * Decrease tau values for ethanol * Move shrink logic and set tau after * Testing tau values and NVT equilibration period after shrink * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add smaller dt for ethanol * Move tau value out of conditionals, fix prints * Improve logging log all energy values, write out raw data to "-raw" file so that there is no ambiguity whether the file has been processed or not, add formatting for new headers * Add tracking for the git commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Add more steps --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com> --- environment.yml | 2 + .../src/engines/hoomd/project.py | 158 +++++++++++++----- 2 files changed, 114 insertions(+), 46 deletions(-) diff --git a/environment.yml b/environment.yml index e5cd75cb..ab5ba874 100644 --- a/environment.yml +++ b/environment.yml @@ -6,6 +6,8 @@ channels: dependencies: - constrainmol - ele + - freud + - gitpython - foyer=0.11.2 - freud=2.6.2 - gmso diff --git a/reproducibility_project/src/engines/hoomd/project.py b/reproducibility_project/src/engines/hoomd/project.py index 2c7d8cf7..aaf9758b 100644 --- a/reproducibility_project/src/engines/hoomd/project.py +++ b/reproducibility_project/src/engines/hoomd/project.py @@ -10,6 +10,25 @@ rigid_molecules = ["waterSPCE", "benzeneUA"] +header_dict = { + "Simulationtimestep": "timestep", + "Simulationtps": "tps", + "mdcomputeThermodynamicQuantitieskinetic_energy": "kinetic_energy", + "mdcomputeThermodynamicQuantitiespotential_energy": "potential_energy", + "mdcomputeThermodynamicQuantitiespressure": "pressure", + "mdcomputeThermodynamicQuantitieskinetic_temperature": "temperature", + "mdcomputeThermodynamicQuantitiesvolume": "volume", + "mdpairLJenergy": "LJ_energy", + "mdpairEwaldenergy": "Ewald_energy", + "mdlong_rangepppmCoulombenergy": "Coulomb_energy", + "mdspecial_pairLJenergy": "LJ_1-4_energy", + "mdspecial_pairCoulombenergy": "Coulomb_1-4_energy", + "mdbondHarmonicenergy": "bond_energy", + "mdangleHarmonicenergy": "angle_energy", + "mddihedralOPLSenergy": "dihedral_energy", + "Statustime_remaining": "time_remaining", +} + class Project(FlowProject): """Subclass of FlowProject to provide custom methods and attributes.""" @@ -96,15 +115,17 @@ def post_process(job): import numpy.lib.recfunctions as rf import unyt as u - for logfile in [job.fn("log-npt.txt"), job.fn("log-nvt.txt")]: - # Make a copy, just in case - backup = f"{logfile}.bkup" - if not os.path.exists(backup): - copy(logfile, backup) + for filename in ["log-npt-raw.txt", "log-nvt-raw.txt"]: + rawlogfile = job.fn(filename) + logfile = job.fn(filename.replace("-raw", "")) - data = np.genfromtxt(logfile, names=True) + data = np.genfromtxt(rawlogfile, names=True) data = clean_data(data) + # Clean up headers + for k, v in header_dict.items(): + data = rf.rename_fields(data, {k: v}) + system_mass = job.sp.mass * u.amu * job.sp.N_liquid volume = data["volume"] * u.nm**3 density = (system_mass / volume).to("g/cm**3") @@ -112,7 +133,6 @@ def post_process(job): pressure_factor = float((1 * u.kJ / u.mol / u.nm**3).to("kPa")) data = rf.drop_fields(data, ["time_remaining"]) - data = rf.rename_fields(data, {"kinetic_temperature": "temperature"}) data["temperature"] /= kB data["pressure"] *= pressure_factor data = rf.append_fields( @@ -125,6 +145,7 @@ def post_process(job): def run_hoomd(job, method, restart=False): """Run a simulation with HOOMD-blue.""" import foyer + import git import gsd.hoomd import hoomd import hoomd.md @@ -139,7 +160,10 @@ def run_hoomd(job, method, restart=False): from reproducibility_project.src.utils.forcefields import load_ff from reproducibility_project.src.utils.rigid import moit + repo = git.Repo(search_parent_directories=True) + sha = repo.head.object.hexsha print(job.sp.molecule) + print(f"git commit: {sha}\n") if method not in ["npt", "nvt", "shrink"]: raise ValueError("Method must be 'nvt', 'npt' or 'shrink'.") @@ -148,6 +172,7 @@ def run_hoomd(job, method, restart=False): # Only the number matters at this point--all other attributes of the # snapshot will be adjusted later. if job.sp["molecule"] in rigid_molecules: + print("Rigid body") isrigid = True init_snap = hoomd.Snapshot() init_snap.particles.types = ["R"] @@ -185,14 +210,24 @@ def run_hoomd(job, method, restart=False): init_snap=init_snap, pppm_kwargs={"Nx": 64, "Ny": 64, "Nz": 64, "order": 7}, ) + print("Snapshot created") - # update the neighborlist exclusions for pentane and benzene - # these wont be set automatically because their scaling is 0 - # forcefield[0] is LJ pair force and all nlist objects are connected - if job.sp.molecule == "benzeneUA" or job.sp.molecule == "pentaneUA": - forcefield[0].nlist.exclusions = ["bond", "1-3", "1-4"] - if job.sp.molecule == "methaneUA": - forcefield[0].nlist.exclusions = [] + # If the molecule is constrained, add distance constraints to + # bonded particles in snapshot + if "constrain" in job.sp.molecule: + print("Constrained bonds") + snapshot.constraints.N = snapshot.bonds.N + snapshot.constraints.group[:] = snapshot.bonds.group[:] + constraint_vals = np.ones(snapshot.bonds.N) * 0.154 + snapshot.constraints.value[:] = constraint_vals + + # I also checked that the starting positions on each bond were + # close enough to the constraint value: + # bond_pos = snapshot.particles.position[snapshot.bonds.group] + # bond_dists = np.linalg.norm(bond_pos[:,0] - bond_pos[:,1], axis=1) + # np.allclose(constraint_vals, bond_dists) + + constrain_dist = hoomd.md.constrain.Distance() # Adjust the snapshot rigid bodies if isrigid: @@ -239,8 +274,17 @@ def run_hoomd(job, method, restart=False): forcefield.remove(f) # update the neighborlist exclusions for rigid + # forcefield[0] is LJ pair force and all nlist objects are connected forcefield[0].nlist.exclusions = ["body"] + # update the neighborlist exclusions for pentane and methane + # pentane's wont be set automatically because the scaling is 0 + # and the default (bond, 1-3) is unecessary and raises a warning for methane + if job.sp.molecule.startswith("pentane"): + forcefield[0].nlist.exclusions = ["bond", "1-3", "1-4"] + elif job.sp.molecule == "methaneUA": + forcefield[0].nlist.exclusions = [] + if job.sp.get("long_range_correction") == "energy_pressure": for force in forcefield: if isinstance(force, hoomd.md.pair.LJ): @@ -357,34 +401,48 @@ def run_hoomd(job, method, restart=False): status = Status(sim) logger[("Status", "time_remaining")] = (status, "time_remaining", "string") + + for f in forcefield: + logger.add(f, quantities=["energy"]) + table_file = hoomd.write.Table( output=open( - job.fn(f"log-{method}.txt"), mode=f"{writemode}", newline="\n" + job.fn(f"log-{method}-raw.txt"), mode=f"{writemode}", newline="\n" ), trigger=hoomd.trigger.Periodic(period=1000), logger=logger, - max_header_len=7, ) sim.operations.writers.append(table_file) - dt = 0.001 + if job.sp.molecule == "ethanolAA": + # ethanol needs a smaller timestep to capture fast oscillations of + # explicit hydrogen bonds (period 0.0118 time units) + dt = 0.0005 + else: + dt = 0.001 if isrigid: integrator = hoomd.md.Integrator(dt=dt, integrate_rotational_dof=True) integrator.rigid = rigid else: integrator = hoomd.md.Integrator(dt=dt) + if "constrain" in job.sp.molecule: + integrator.constraints = [constrain_dist] integrator.forces = forcefield # convert temp in K to kJ/mol - kT = (job.sp.temperature * u.K).to_equivalent("kJ/mol", "thermal").value + kT = float( + (job.sp.temperature * u.K).to_equivalent("kJ/mol", "thermal").value + ) + print(f"kT = {kT}") # start with high tau and tauS - tau = 1000 * dt - tauS = 5000 * dt + tau = 0.5 # 1000dt (ethanol) or 500dt + tauS = 1 # 2000dt (ethanol) or 1000dt if method == "npt": # convert pressure to unit system - pressure = (job.sp.pressure * u.kPa).to("kJ/(mol*nm**3)").value + pressure = float((job.sp.pressure * u.kPa).to("kJ/(mol*nm**3)").value) + print(f"Pressure = {pressure}") integrator_method = hoomd.md.methods.NPT( filter=_all, kT=kT, @@ -407,27 +465,25 @@ def run_hoomd(job, method, restart=False): if not restart: steps = 1e6 print( - f"""Running {steps} with tau: {integrator.methods[0].tau} and - tauS: {integrator.methods[0].tauS}""" + f"Running {steps:.0e} with tau: {integrator.methods[0].tau} " + f"and tauS: {integrator.methods[0].tauS}" ) sim.run(steps) print("Done") - integrator.methods[0].tauS = 1000 * dt - integrator.methods[0].tau = 100 * dt - else: - # Shrink and NVT both use NVT method - if method == "shrink": - # shrink to the desired box length - L = job.sp.box_L_liq - shrink_steps = 1e5 - else: - # The target volume should be the average volume from NPT - target_volume = job.doc.avg_volume - L = target_volume ** (1 / 3) - shrink_steps = 2e4 + else: if not restart: - # Shrink and nvt methods both use shrink step + # Shrink and NVT both use NVT method + if method == "shrink": + # shrink to the desired box length + L = job.sp.box_L_liq + shrink_steps = 1e5 + else: + # The target volume should be the average volume from NPT + target_volume = job.doc.avg_volume + L = target_volume ** (1 / 3) + shrink_steps = 2e4 + # Shrink step follows this example # https://hoomd-blue.readthedocs.io/en/latest/tutorial/ # 01-Introducing-Molecular-Dynamics/03-Compressing-the-System.html @@ -445,24 +501,32 @@ def run_hoomd(job, method, restart=False): ) sim.operations.updaters.append(box_resize) print( - f"Running shrink {shrink_steps} with tau: {integrator.methods[0].tau}" + f"Running shrink {shrink_steps:.0e} with tau: " + f"{integrator.methods[0].tau}" ) sim.run(shrink_steps + 1) print("Done") assert sim.state.box == final_box sim.operations.updaters.remove(box_resize) - integrator.methods[0].tau = 100 * dt + integrator.methods[0].tau = 0.1 if method != "shrink": - steps = 5e6 + steps = 2e7 if method == "npt": + integrator.methods[0].tauS = 1 print( - f"""Running {steps} with tau: {integrator.methods[0].tau} and - tauS: {integrator.methods[0].tauS}""" + f"Running {steps:.0e} with tau: {integrator.methods[0].tau} " + f"and tauS: {integrator.methods[0].tauS}" ) else: - print(f"Running {steps} with tau: {integrator.methods[0].tau}") + print(f"Running {steps:.0e} with tau: {integrator.methods[0].tau}") + sim.run(steps) + else: + # Try adding a short temperature equilibration step after shrink + steps = 1e4 + print(f"Running {steps:.0e} with tau: {integrator.methods[0].tau}") sim.run(steps) + job.doc[f"{method}_finished"] = True print("Finished", flush=True) @@ -474,9 +538,9 @@ def check_equilibration(job, method, eq_property, min_t0=100): import reproducibility_project.src.analysis.equilibration as eq - data = np.genfromtxt(job.fn(f"log-{method}.txt"), names=True) + data = np.genfromtxt(job.fn(f"log-{method}-raw.txt"), names=True) data = clean_data(data) - prop_data = data[eq_property] + prop_data = data[f"mdcomputeThermodynamicQuantities{eq_property}"] iseq, _, _, _ = eq.is_equilibrated(prop_data) if iseq: uncorr, t0, g, N = eq.trim_non_equilibrated(prop_data) @@ -497,7 +561,9 @@ def clean_data(data): The HOOMD Table file writer always writes a header, but for restarted jobs, this header is in the middle of the file, which creates nan values. """ - return np.delete(data, np.where(np.isnan(data["timestep"]))[0], axis=0) + return np.delete( + data, np.where(np.isnan(data["Simulationtimestep"]))[0], axis=0 + ) class Status: