radonpy/radonpy

RadonPy is a Python library to automate physical property calculations for polymer informatics.

radonpy's Issues

psi4のマルチプロセスでの動作について

@yhayashi1986
下記フォークにてRISを実装しています
https://github.com/ryuichi-sakashita/RadonPyRIS

Slackにも報告したとおり、
二面角のスキャンはできました
その後の二面角×3の全組み合わせを計算するときにPsi4がプロセスごと落ちてしまいます

別プロセスとすることでエラーをキャッチしようとしましたが、
今度はサブプロセスとしてPsi4を動かすときにPsi4に下記の原因不明のエラーが出るようです

RadonPy info: Psi4 optimization is running...
forrtl: severe (174): SIGSEGV, segmentation fault occurred

変更点：
RISメイン処理：sim/preset/ris.py
sim/psi4_wrapper.pyに　localminima_dihedrals_scan(self, dihedral, step=15, **kwargs)を追加
実行スクリプト：sample_script/ris_test.py　←これを実行したら再現できると思います

お手すきのときに見ていただけたら幸いです

Adding new atom types

Radonpy is an easy tool for creating MD input. I could generate ff for molecules and polymers. I'm interested in generating a force field for a metal oxide cluster. Is it feasible to load force fields for this system and combine them with polymers/molecules?

About the parameters in sample_script

Hi there!
I am trying to understand the code of sample_script repo.
However, I find it out that the data dictionary has a piece of code os.environ.get('RadonPy_DBID').

Should I have a database preparation before I start the code?
Otherwise, it may report
smi_list = data['smiles_list'].split(',') AttributeError: 'NoneType' object has no attribute 'split'

Hope you may drop me a line.

TypeError in quick_rw when using poly.polymerize_rw with LAMMPS

I find a TypeError when using the poly.polymerize_rw function. The error occurs in the quick_rw function during the invocation of md.add_md():
TypeError: add_md() missing 1 required positional argument: 'step'
I think the issue lies in the quick_rw function, in this line:
md.add_md('nve', step, time_step=time_step, shake=shake, nve_limit=limit, **kwargs)
The step parameter should be passed as a keyword argument to avoid confusion, like so:
md.add_md('nve', step=step, time_step=time_step, shake=shake, nve_limit=limit, **kwargs)
Thank you very much

KeyError: 'AtomicCharge' when running equilibrium md functions

Hello,

Thank you for writing this package. It's a very exciting tool!

I have a question about forcefield assignment at the polymer level.

I'm running the following test on polystyrene now following the tutorial pdf:

from radonpy.core import poly, utils
from radonpy.sim import qm
from radonpy.ff.gaff2_mod import GAFF2_mod
from radonpy.sim.preset import eq
import os

cpus = utils.cpu_count()

ps_smiles = 'CC()c1ccccc1'
mol = utils.mol_from_smiles(ps_smiles)

work_dir = 'path/to/work/dir'

ff = GAFF2_mod()
mol, energy = qm.conformation_search(mol,
ff=ff,
work_dir = work_dir
)

qm.assign_charges(mol,
charge='RESP',
work_dir=work_dir
)

repeat_units = 10
atom_nubmer = monomer_atom_num*repeat_units
print(atom_nubmer)

atom_number = 1000
ter = utils.mol_from_smiles('*C')
n = poly.calc_n_from_num_atoms(mol,
atom_number ,
terminal1=ter
)
homopoly = poly.polymerize_rw(mol,
n,
tacticity='atactic'
)
homopoly = poly.terminate_rw(homopoly,
ter)

result = ff.ff_assign(homopoly)

It seems that the forcefield is assigned at the conformation search level. Is there a reason it needs to be reassigned after polymerization? Is there a way to pass the forcefield information from the qm calculations to the polymerize function? More importantly, the partial charges from the charge calculation are not transferred from the monomers to the polymer. This leads to the following key error when you try to run the md equilibration.

n_chains = 10
ac = poly.amorphous_cell(homopoly,
n_chains
)

temp = 300 # K
press = 1.0 # bar
eqmd = eq.EQ21step(ac,
work_dir = work_dir)
ac = eqmd.exec(temp = temp,
press = press,
omp = 1,
gpu = 2,
mpi = utils.cpu_count())

KeyError Traceback (most recent call last)
Cell In[16], line 5
2 press = 1.0 # bar
3 eqmd = eq.EQ21step(ac,
4 work_dir = work_dir)
----> 5 ac = eqmd.exec(temp = temp,
6 press = press,
7 omp = 1,
8 gpu = 2,
9 mpi = utils.cpu_count())

**File anaconda3/envs/radonpy_py311/lib/python3.11/site-packages/radonpy/sim/preset/eq.py:351, in EQ21step.exec(self, confId, f_density, max_temp, temp, press, max_press, step_list, press_ratio, time_step, eq_step, omp, mpi, gpu, intel, opt, **kwargs)
349 utils.MolToPDBFile(self.mol, os.path.join(self.work_dir, self.pdb_file))
350 lmp = lammps.LAMMPS(work_dir=self.work_dir, solver_path=self.solver_path)
--> 351 lmp.make_dat(self.mol, file_name=self.dat_file1, confId=confId)
353 dt1 = datetime.datetime.now()
354 utils.radon_print('Packing simulation (eq1) by LAMMPS is running...', level=1)

File anaconda3/envs/radonpy_py311/lib/python3.11/site-packages/radonpy/sim/lammps.py:333, in LAMMPS.make_dat(self, mol, confId, file_name, dir_name, velocity, temp, drude)
331 dir_name = dir_name if dir_name is not None else self.work_dir
332 dat_file = os.path.join(dir_name, file_name)
--> 333 MolToLAMMPSdata(mol, dat_file, confId=confId, velocity=velocity, temp=temp, drude=drude)
335 return dat_file
...
2755 coord[i][0], coord[i][1], coord[i][2]))
2757 if velocity:
2758 lines.append('')

KeyError: 'AtomicCharge'**

The work around to this is to recalculate the charge after polymerization by running result = ff.ff_assign(homopoly, charge='RESP'), but redoing the qm calculations of partial charges at the polymer level becomes prohibitively expensive as the number of monomers increases. Is there a way to pass the ff and partial charges from the monomer to the polymer mol structure so that these calculations do not have to be redone?

Thanks!
Mike Boyle

Usage of package OPENMP

Hello
Thanks for your repo! it 's a really useful tool for us who don't understand simulation very much
But i came across a situation when trying the tutorial as

''RadonPy warning: OPENMP package is not available. Parallel number of OPENMP is changed to zero.''

I have tired command

'conda install -c conda-forge openmpi '

but it doesn't work, it seemd like i still fail to install some of the necessary packages, so how can i solve this problem?
Looking forward for your reply! Thanks!

Calculate FF descriptor for small molecule?

In the present implementation, is it possible to calculate FF descriptor for small molecules (without connection atoms)? If not, will it be expanded to do so?