Michal Krompiec

bug in PeriodicForce

3

file TensorMol/ForceModifiers/Periodic.py line 400: return etore, ftore should be changed to: if (DoForce): return etore, ftore else: return etore

bug in Periodic.py?

1

I'm trying to run an MD simulation in PBC, using ChemSpider-trained network: def EnAndForce(z_, x_, nreal_, DoForce = True): mtmp = Mol(z_,x_) en,f = manager.EvalBPDirectEEUpdateSinglePeriodic(mtmp, PARAMS["AN1_r_Rc"], PARAMS["AN1_a_Rc"], PARAMS["EECutoffOff"], nreal_,True) return...

DUCC is not parallelized

3

**Describe the bug** Hamiltonian downfolding in DUCC (nwchem/src/tce/ducc/ducc.F) runs on 1 thread, regardless of number of OMP threads or MPI processes. Calculation of the CCSD amplitudes is (obviously) parallelized but...

Can you share a code example (recipe) for building a generative model with GenerativeRNN?

2D PBC

3

**Is your feature request related to a problem? Please describe.** Calculations of periodic surfaces require either 2D PBC or some correction scheme to eliminate Coulombic and dispersion interaction between surfaces...

Potential energy without MTD potential in MTD trajectories

2

In the trajectory file from a metadynamics run, the potential energy printed is the "full" metadynamics energy, including the RMSD bias potential (and possibly also reactor wall potential). For analysis...

TrajectoryTrainer doesn't use energies for training

1

**Is your feature request related to a problem? Please describe.** GP from AIMD trainer (TrajectoryTrainer) uses only forces, not energies, for training. **Describe the solution you'd like** An option to...

issues with homebrew installation

1

I get the following error when trying to install on macOS, would be grateful for any advice: ``` cabal v2-install --jobs=8 --max-backjumps=100000 --install-method=copy --installdir=/opt/homebrew/Cellar/camfort/1.1.2/bin Error: cabal: Could not resolve dependencies:...

Hessian in TorsionTarget?

3

I'm looking for ways to speed up torsion fitting. Is the Hessian of the objective function computed for the TorsionTarget if Newton-Raphson optimizer is used? Should BFGS be faster?

optimizer crash

4

For certain molecules, we are getting this error reproducibly: Unknown Error: Traceback (most recent call last): File "/sw-pmpv/sdk/anaconda-python/2020.07/envs/anaconda-2020/lib/python3.8/site-packages/geometric/optimize.py", line 1893, in main run_optimizer(**vars(args)) File "/sw-pmpv/sdk/anaconda-python/2020.07/envs/anaconda-2020/lib/python3.8/site-packages/geometric/optimize.py", line 1821, in run_optimizer progress...