Subclass of Target for lipid property matching.
More...
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| def | __init__ (self, options, tgt_opts, forcefield) |
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| def | prepare_temp_directory (self) |
| | Prepare the temporary directory by copying in important files. More...
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| def | read_data (self) |
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| def | check_files (self, there) |
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| def | npt_simulation (self, temperature, pressure, simnum) |
| | Submit a NPT simulation to the Work Queue. More...
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| def | polarization_correction (self, mvals) |
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| def | indicate (self) |
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| def | objective_term (self, points, expname, calc, err, grad, name="Quantity", SubAverage=False) |
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| def | submit_jobs (self, mvals, AGrad=True, AHess=True) |
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| def | get (self, mvals, AGrad=True, AHess=True) |
| | Fitting of lipid bulk properties. More...
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Subclass of Target for lipid property matching.
Definition at line 57 of file lipid.py.
◆ __init__()
| def src.lipid.Lipid.__init__ |
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self, |
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options, |
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tgt_opts, |
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forcefield |
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◆ check_files()
| def src.lipid.Lipid.check_files |
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self, |
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there |
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◆ get()
| def src.lipid.Lipid.get |
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self, |
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mvals, |
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AGrad = True, |
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AHess = True |
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Fitting of lipid bulk properties.
This is the current major direction of development for ForceBalance. Basically, fitting the QM energies / forces alone does not always give us the best simulation behavior. In many cases it makes more sense to try and reproduce some experimentally known data as well.
In order to reproduce experimentally known data, we need to run a simulation and compare the simulation result to experiment. The main challenge here is that the simulations are computationally intensive (i.e. they require energy and force evaluations), and furthermore the results are noisy. We need to run the simulations automatically and remotely (i.e. on clusters) and a good way to calculate the derivatives of the simulation results with respect to the parameter values.
This function contains some experimentally known values of the density and enthalpy of vaporization (Hvap) of lipid water. It launches the density and Hvap calculations on the cluster, and gathers the results / derivatives. The actual calculation of results / derivatives is done in a separate file.
After the results come back, they are gathered together to form an objective function.
- Parameters
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| [in] | mvals | Mathematical parameter values |
| [in] | AGrad | Switch to turn on analytic gradient |
| [in] | AHess | Switch to turn on analytic Hessian |
- Returns
- Answer Contribution to the objective function Fill in the weight matrix with MBAR weights where MBAR was run, and equal weights otherwise.
Definition at line 550 of file lipid.py.
◆ indicate()
| def src.lipid.Lipid.indicate |
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self | ) |
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◆ npt_simulation()
| def src.lipid.Lipid.npt_simulation |
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self, |
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temperature, |
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pressure, |
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simnum |
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Submit a NPT simulation to the Work Queue.
Definition at line 321 of file lipid.py.
◆ objective_term()
| def src.lipid.Lipid.objective_term |
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self, |
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points, |
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expname, |
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calc, |
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err, |
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grad, |
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name = "Quantity", |
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SubAverage = False |
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◆ polarization_correction()
| def src.lipid.Lipid.polarization_correction |
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self, |
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mvals |
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◆ prepare_temp_directory()
| def src.lipid.Lipid.prepare_temp_directory |
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self | ) |
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Prepare the temporary directory by copying in important files.
Definition at line 189 of file lipid.py.
◆ read_data()
| def src.lipid.Lipid.read_data |
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self | ) |
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◆ submit_jobs()
| def src.lipid.Lipid.submit_jobs |
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self, |
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mvals, |
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AGrad = True, |
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AHess = True |
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◆ do_self_pol
| src.lipid.Lipid.do_self_pol |
◆ engname
◆ extra_output
| src.lipid.Lipid.extra_output |
◆ gas_engine
| src.lipid.Lipid.gas_engine |
◆ Gp
◆ Labels
◆ last_traj
| src.lipid.Lipid.last_traj |
◆ lipid_mol
| src.lipid.Lipid.lipid_mol |
◆ lipid_mols
| src.lipid.Lipid.lipid_mols |
◆ lipid_mols_new
| src.lipid.Lipid.lipid_mols_new |
◆ loop_over_snapshots
| src.lipid.Lipid.loop_over_snapshots |
LPW 2018-02-11: This is set to True if the target calculates a single-point property over several existing snapshots.
Definition at line 123 of file lipid.py.
◆ MBarEnergy
| src.lipid.Lipid.MBarEnergy |
Evaluated energies for all trajectories (i.e.
all iterations and all temperatures), using all mvals
Definition at line 185 of file lipid.py.
◆ Objective
| src.lipid.Lipid.Objective |
◆ PhasePoints
| src.lipid.Lipid.PhasePoints |
◆ Pp
◆ read_indicate
| src.lipid.Lipid.read_indicate |
◆ read_objective
| src.lipid.Lipid.read_objective |
◆ RefData
◆ SavedMVal
| src.lipid.Lipid.SavedMVal |
Saved force field mvals for all iterations.
Definition at line 181 of file lipid.py.
◆ SavedTraj
| src.lipid.Lipid.SavedTraj |
Saved trajectories for all iterations and all temperatures.
Definition at line 183 of file lipid.py.
◆ w_al
◆ w_alpha
◆ w_cp
◆ w_eps0
◆ w_kappa
◆ w_lkappa
◆ w_rho
Density.
Ignore enthalpy. Thermal expansion coefficient. Isothermal compressibility. Isobaric heat capacity. Static dielectric constant. Average area per lipid Bilayer Isothermal compressibility. Deuterium order parameter Estimation of errors.
Definition at line 803 of file lipid.py.
◆ w_scd
◆ Wp
◆ write_indicate
| src.lipid.Lipid.write_indicate |
◆ Xp
The documentation for this class was generated from the following file:
1.8.13