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mosdef-hub
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mbuild
A hierarchical, component based molecule builder
https://mbuild.mosdef.org
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add "metal" Unit for Lammps
#1098
thangckt
closed
1 year ago
6
print the hierarchy of a compound
#1097
chrisiacovella
closed
1 year ago
4
Plot hierarchy of a compound
#1096
chrisiacovella
closed
1 year ago
0
Write LJ parameters with 5 decimal places instead of 3 with MCF writer.
#1095
rwsmith7531
closed
1 year ago
1
Mcf lj precision
#1094
rwsmith7531
closed
1 year ago
0
Cassandra mcf writer uses fewer decimal places for LJ parameters than other writers.
#1093
rwsmith7531
closed
1 year ago
0
Change dihedral phi to integer in lammpsdata.py as required by LAMMPS.
#1092
rwsmith7531
closed
1 year ago
2
Dihedral phi in lammpsdata writer is incorrectly written as a float
#1091
rwsmith7531
closed
1 year ago
1
CI stops running because tests are using too much memory.
#1090
chrisiacovella
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#1089
pre-commit-ci[bot]
closed
1 year ago
1
Issue 1080
#1088
RainierBarrett
closed
1 year ago
1
replaced bondgraph with networkx
#1087
chrisiacovella
closed
1 year ago
5
Lammps lj unit charges
#1086
jaclark5
closed
1 year ago
1
lammpsdatawrite prevent scaling of LJ unit charges
#1085
jaclark5
closed
1 year ago
0
Improved performance of bond look up
#1084
chrisiacovella
closed
1 year ago
2
[pre-commit.ci] pre-commit autoupdate
#1083
pre-commit-ci[bot]
closed
1 year ago
1
Compound.bonds() performance prohibitively slow as system size increases
#1082
chrisiacovella
closed
1 year ago
3
kwargs not passed from compound.to_gmso to conversion.to_gmso
#1081
chrisiacovella
closed
1 year ago
0
Different behavior in `fill_box` and `fill_region`. `fill_region` errors when using a list of Compounds
#1080
chrisjonesBSU
closed
1 year ago
5
[pre-commit.ci] pre-commit autoupdate
#1079
pre-commit-ci[bot]
closed
1 year ago
1
updating open babel energy minimization to no longer use temp file
#1078
chrisiacovella
closed
1 year ago
6
OpenBabel energy minimization fails if Compound.name does not contain an element symbol
#1077
chrisiacovella
closed
1 year ago
0
Fixing energy minimization tests
#1076
chrisiacovella
closed
1 year ago
2
[pre-commit.ci] pre-commit autoupdate
#1075
pre-commit-ci[bot]
closed
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#1074
pre-commit-ci[bot]
closed
1 year ago
1
Lammps molecule number
#1073
jaclark5
closed
1 year ago
25
Cannot number compounds in write_lammpsdata
#1072
jaclark5
closed
1 year ago
0
Reorder bond, angle, and dihedral in write_lammpsdata
#1071
jaclark5
closed
1 year ago
12
Order bonds, angles, and dihedrals consistently for lammpsdata files
#1070
jaclark5
closed
1 year ago
9
Produce n=2 when ports are not capped
#1069
jaclark5
closed
1 year ago
1
When Alkane(n=2, cap_front=False, cap_end=False) the output is n=1
#1068
jaclark5
closed
1 year ago
0
Turn off fail-fast
#1067
daico007
closed
1 year ago
1
Patches for element reading in lattice builder
#1066
CalCraven
closed
1 year ago
2
The lattice builder won't check for element information if loaded from CIF
#1065
CalCraven
closed
1 year ago
0
Migrate GOMC and CHARMM writer
#1064
daico007
closed
1 year ago
6
[pre-commit.ci] pre-commit autoupdate
#1063
pre-commit-ci[bot]
closed
1 year ago
1
Add more notes about unit conversions to the hoomd functions
#1062
chrisjonesBSU
closed
1 year ago
1
Updates to energy minimization routines
#1061
chrisiacovella
closed
1 year ago
3
Add CodeQL workflow for GitHub code scanning
#1060
lgtm-com[bot]
closed
1 year ago
2
Fix bug related to `get_boundingbox()`
#1059
daico007
closed
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#1058
pre-commit-ci[bot]
closed
1 year ago
1
Charge units for create_hoomd_forcefield
#1057
scmartin
closed
1 year ago
5
Add smiles string conversion using pybel backend
#1056
daico007
closed
1 year ago
2
drop py3.7 from testing
#1055
daico007
closed
2 years ago
2
Trim coordinate_transform.py, new features for spin method
#1054
daico007
closed
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#1053
pre-commit-ci[bot]
closed
2 years ago
1
mbuild.Compound.energy_minimize() function fails if a GMSO formatted XML is used
#1052
bc118
opened
2 years ago
1
add refer_inhierarchy to gmso conversion
#1051
daico007
closed
2 years ago
2
change utils/conversion.py function name "RB_to_CHARMM" --> "RB_to_periodic"
#1050
bc118
closed
2 months ago
1
Fix for bug with mbuild missing edges in bond graph
#1049
CalCraven
closed
2 years ago
2
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