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Hotfix in BCC parametrization #73

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merged 20 commits into from
Nov 29, 2022
Merged

Hotfix in BCC parametrization #73

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5e0d2c7
add support for SMIRKS, bcc and virtual site
Ericwang6 Nov 20, 2022
d17736a
add dependencies in ut workflow
Ericwang6 Nov 20, 2022
6c4e916
Merge branch 'devel' of https://github.com/deepmodeling/DMFF into smirks
Ericwang6 Nov 20, 2022
41da2ba
add interface to obtain topmat
Ericwang6 Nov 21, 2022
aa02e2a
code clean
Ericwang6 Nov 21, 2022
d756b56
fix multiple matches_dict var
Ericwang6 Nov 21, 2022
eee1604
add tests for building top
Ericwang6 Nov 21, 2022
0d148e0
add tests for smirks/bcc/vsite
Ericwang6 Nov 21, 2022
4ab27f5
add dockerfile for dev env
Ericwang6 Nov 21, 2022
96df0e6
add examples of smirks
Ericwang6 Nov 22, 2022
3438b8e
add usage of smirks in doc
Ericwang6 Nov 22, 2022
938a411
rm api doc in _date/_version
Ericwang6 Nov 22, 2022
c2df0d8
fix typo
Ericwang6 Nov 22, 2022
78b78ac
update (doc): architecture img
Ericwang6 Nov 25, 2022
34606ae
update (README): citation and code structure
Ericwang6 Nov 25, 2022
7cb36da
update (doc): bad rendered latex
Ericwang6 Nov 25, 2022
fbdcf88
update (doc): typo in usage
Ericwang6 Nov 25, 2022
5d329cc
update (doc): smirks in XML
Ericwang6 Nov 25, 2022
4436948
update (smirks): change bcc err to warning
Ericwang6 Nov 29, 2022
fbfd023
resolve conflicts
Ericwang6 Nov 29, 2022
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6 changes: 3 additions & 3 deletions dmff/generators/classical.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from collections import defaultdict
from typing import Dict
from copy import deepcopy
import warnings

import numpy as np
import jax.numpy as jnp
Expand Down Expand Up @@ -755,7 +755,7 @@ def addVsiteFunc(pos, params):
self.top_mat[query2[0], nnode] += 1
self.top_mat[query2[1], nnode] -= 1
else:
raise DMFFException(
warnings.warn(
f"No BCC parameter for bond between Atom{beginAtomIdx} and Atom{endAtomIdx}"
)
else:
Expand Down Expand Up @@ -1191,4 +1191,4 @@ def getJaxPotential(self):
return self._jaxPotential


dmff.api.jaxGenerators["LennardJonesForce"] = LennardJonesGenerator
dmff.api.jaxGenerators["LennardJonesForce"] = LennardJonesGenerator