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Update Documentation and Prepare for 1.1.0 #76

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Update Documentation and Prepare for 1.1.0 #76

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53cee01
Update documentation
ajfriedman22 Feb 4, 2025
5307156
Update function documentation
ajfriedman22 Feb 4, 2025
3801e04
add an alpine specific environment file
ajfriedman22 Feb 11, 2025
5b49b67
Update environment.yml
ajfriedman22 Feb 11, 2025
58ddebf
Update environment.yml
ajfriedman22 Feb 11, 2025
904df2f
Update alpine.yml
ajfriedman22 Feb 11, 2025
d7489b8
update docs
ajfriedman22 Feb 28, 2025
fd63fd9
update tutorial
ajfriedman22 Mar 14, 2025
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9 changes: 9 additions & 0 deletions alpine.yml
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# Set-up ensemble_md on Alpine Cluster
name: REXEE
dependencies:
- openmpi
- mpi4py
- python =3.11.*
- pip
- pip:
- -e .
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2,055 changes: 2,055 additions & 0 deletions docs/examples/tutorial_2/A-B.gro
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158 changes: 158 additions & 0 deletions docs/examples/tutorial_2/A-B.itp
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[ moleculetype ]
; Name nrexcl
A2B 3

[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 ss 1 A2B S1 1 -0.116300 32.0600
2 cc 1 A2B C2 2 0.402700 12.0100
3 nd 1 A2B N3 3 -0.636000 14.0100 nd -0.634000 14.0100
4 cd 1 A2B C4 4 0.333200 12.0100 cd 0.332200 12.0100
5 cc 1 A2B C5 5 -0.252400 12.0100 cc -0.251400 12.0100
6 c3 1 A2B C6 6 -0.131400 12.0100 c3 -0.110700 12.0100
7 h4 1 A2B H1 7 0.044100 1.0080 h4 0.043100 1.0080
8 h4 1 A2B H2 8 0.180000 1.0080
9 hc 1 A2B H3 9 0.058700 1.0080 hc 0.057250 1.0080
10 hc 1 A2B H4 10 0.058700 1.0080 hc 0.057250 1.0080
11 hc 1 A2B H17 11 0.058700 1.0080 DUM_hc 0.000000 1.0080
12 DUM_c3 1 A2B DC7 12 0.000000 12.0100 c3 -0.089100 12.0100
13 DUM_hc 1 A2B HV5 13 0.000000 1.0080 hc 0.043000 1.0080
14 DUM_hc 1 A2B HV6 14 0.000000 1.0080 hc 0.043000 1.0080
15 DUM_hc 1 A2B HV7 15 0.000000 1.0080 hc 0.043000 1.0080

[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1 0.175380 193853.088000 0.175380 193853.088000
1 5 1 0.175380 193853.088000 0.175380 193853.088000
2 3 1 0.131580 351221.696000 0.131580 351221.696000
2 6 1 0.150020 213501.152000 0.150020 213501.152000
3 4 1 0.137130 289474.224000 0.137130 289474.224000
4 5 1 0.137300 323205.632000 0.137300 323205.632000
4 7 1 0.108180 307348.272000 0.108180 307348.272000
5 8 1 0.108090 308544.896000 0.108090 308544.896000
6 9 1 0.109620 288905.200000 0.109620 288905.200000
6 10 1 0.109620 288905.200000 0.109620 288905.200000
6 11 1 0.109620 288905.200000 0.109620 288905.200000
6 12 1 0.153540 191535.152000 0.153540 191535.152000
12 13 1 0.109620 288905.200000 0.109620 288905.200000
12 14 1 0.109620 288905.200000 0.109620 288905.200000
12 15 1 0.109620 288905.200000 0.109620 288905.200000

[ pairs ]
; ai aj funct c0 c1 c2 c3
4 6 1
5 6 1
1 9 1
1 10 1
1 11 1
1 7 1
2 8 1
2 7 1
3 9 1
3 10 1
3 11 1
3 8 1
7 8 1
1 12 1
3 12 1
2 13 1
2 14 1
2 15 1
9 13 1
9 14 1
9 15 1
10 13 1
10 14 1
10 15 1

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 116.440050 583.584320 116.440050 583.584320 ; S1 C2 N3
1 2 6 1 121.350052 522.665280 121.350052 522.665280 ; S1 C2 C6
1 5 4 1 111.550048 557.476160 111.550048 557.476160 ; S1 C5 C4
2 1 5 1 90.360039 854.707520 90.360039 854.707520 ; C2 S1 C5
2 3 4 1 105.370045 730.944800 105.370045 730.944800 ; C2 N3 C4
3 2 6 1 123.870053 548.355040 123.870053 548.355040 ; N3 C2 C6
3 4 5 1 111.580048 597.893600 111.580048 597.893600 ; N3 C4 C5
1 5 8 1 120.150052 352.376480 120.150052 352.376480 ; S1 C5 H2
2 6 9 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H3
2 6 10 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H4
2 6 11 1 110.360047 368.526720 110.360047 368.526720 ; C2 C6 H17
3 4 7 1 121.200052 403.337600 121.200052 403.337600 ; N3 C4 H1
4 5 8 1 129.110055 367.773600 129.110055 367.773600 ; C4 C5 H2
5 4 7 1 127.640055 369.865600 127.640055 369.865600 ; C5 C4 H1
9 6 10 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H4
9 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H3 C6 H17
10 6 11 1 107.730046 299.574400 107.730046 299.574400 ; H4 C6 H17
2 6 12 1 112.960048 505.929280 112.960048 505.929280 ; C2 C6 DC7
6 12 13 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV5
6 12 14 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV6
6 12 15 1 109.680047 362.083360 109.680047 362.083360 ; C6 DC7 HV7
12 6 9 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H3
12 6 10 1 109.680047 362.083360 109.680047 362.083360 ; DC7 C6 H4
13 12 14 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV6
13 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV5 DC7 HV7
14 12 15 1 107.730046 299.574400 107.730046 299.574400 ; HV6 DC7 HV7

[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
1 2 3 4 1 180.0000771 19.874 2 180.0000771 0 2 ; S1 C2 N3 C4 (AAAA->AAAA)
1 5 4 3 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 N3 (AAAA->AAAA)
2 1 5 4 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 C4 (AAAA->AAAA)
2 3 4 5 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 C5 (AAAA->AAAA)
5 1 2 3 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 N3 (AAAA->AAAA)
4 3 2 6 1 180.0000771 19.874 2 180.0000771 0 2 ; C4 N3 C2 C6 (AAAA->AAAA)
5 1 2 6 1 180.0000771 4.6024 2 180.0000771 0 2 ; C5 S1 C2 C6 (AAAA->AAAA)
1 2 3 6 4 180.0000771 4.6024 2 180.0000771 0 2 ; S1 C2 N3 C6 (AAAA->AAAA)
1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA)
1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA)
1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD)
1 2 6 11 1 0 0 3 0 0 3 ; S1 C2 C6 H17 (AAAA->AAAD)
1 5 4 7 1 180.0000771 16.736 2 180.0000771 0 2 ; S1 C5 C4 H1 (AAAA->AAAA)
2 1 5 8 1 180.0000771 4.6024 2 180.0000771 0 2 ; C2 S1 C5 H2 (AAAA->AAAA)
2 3 4 7 1 180.0000771 19.874 2 180.0000771 0 2 ; C2 N3 C4 H1 (AAAA->AAAA)
3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA)
3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA)
3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD)
3 2 6 11 1 0 0 3 0 0 3 ; N3 C2 C6 H17 (AAAA->AAAD)
3 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; N3 C4 C5 H2 (AAAA->AAAA)
7 4 5 8 1 180.0000771 16.736 2 180.0000771 0 2 ; H1 C4 C5 H2 (AAAA->AAAA)
1 2 3 4 1 180.0000771 0 2 180.0000771 19.874 2 ; S1 C2 N3 C4 (AAAA->AAAA)
1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA)
1 2 6 12 1 0 0 3 0 0 3 ; S1 C2 C6 DC7 (AAAD->AAAA)
1 5 4 3 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 N3 (AAAA->AAAA)
2 1 5 4 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 C4 (AAAA->AAAA)
2 3 4 5 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 C5 (AAAA->AAAA)
5 1 2 3 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 N3 (AAAA->AAAA)
3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA)
3 2 6 12 1 0 0 3 0 0 3 ; N3 C2 C6 DC7 (AAAD->AAAA)
4 3 2 6 1 180.0000771 0 2 180.0000771 19.874 2 ; C4 N3 C2 C6 (AAAA->AAAA)
5 1 2 6 1 180.0000771 0 2 180.0000771 4.6024 2 ; C5 S1 C2 C6 (AAAA->AAAA)
1 2 3 6 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C2 N3 C6 (AAAA->AAAA)
1 2 6 9 1 0 0 3 0 0 3 ; S1 C2 C6 H3 (AAAA->AAAA)
1 2 6 10 1 0 0 3 0 0 3 ; S1 C2 C6 H4 (AAAA->AAAA)
1 5 4 7 1 180.0000771 0 2 180.0000771 16.736 2 ; S1 C5 C4 H1 (AAAA->AAAA)
2 1 5 8 1 180.0000771 0 2 180.0000771 4.6024 2 ; C2 S1 C5 H2 (AAAA->AAAA)
2 3 4 7 1 180.0000771 0 2 180.0000771 19.874 2 ; C2 N3 C4 H1 (AAAA->AAAA)
2 6 12 13 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV5 (AADD->AAAA)
2 6 12 14 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV6 (AADD->AAAA)
2 6 12 15 1 0 0 3 0 0.6508444 3 ; C2 C6 DC7 HV7 (AADD->AAAA)
3 2 6 9 1 0 0 3 0 0 3 ; N3 C2 C6 H3 (AAAA->AAAA)
3 2 6 10 1 0 0 3 0 0 3 ; N3 C2 C6 H4 (AAAA->AAAA)
3 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; N3 C4 C5 H2 (AAAA->AAAA)
7 4 5 8 1 180.0000771 0 2 180.0000771 16.736 2 ; H1 C4 C5 H2 (AAAA->AAAA)
9 6 12 13 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV5 (AADD->AAAA)
9 6 12 14 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV6 (AADD->AAAA)
9 6 12 15 1 0 0 3 0 0.50208 3 ; H3 C6 DC7 HV7 (AADD->AAAA)
10 6 12 13 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV5 (AADD->AAAA)
10 6 12 14 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV6 (AADD->AAAA)
10 6 12 15 1 0 0 3 0 0.50208 3 ; H4 C6 DC7 HV7 (AADD->AAAA)
5 7 4 3 4 180.0000771 0 2 180.0000771 4.6024 2 ; C5 H1 C4 N3 (AAAA->AAAA)
1 5 8 4 4 180.0000771 0 2 180.0000771 4.6024 2 ; S1 C5 H2 C4 (AAAA->AAAA)

#ifdef POSRES
#include "posre.itp"
#endif
32 changes: 32 additions & 0 deletions docs/examples/tutorial_2/A-B.top
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[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.83333333

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
ss 16 32.060000 0.00000000 A 0.35324134 1.1815616
cc 6 12.010000 0.00000000 A 0.33152123 0.4133792
nd 7 14.010000 0.00000000 A 0.33841679 0.3937144
cd 6 12.010000 0.00000000 A 0.33152123 0.4133792
c3 6 12.010000 0.00000000 A 0.33977095 0.4510352
h4 1 1.008000 0.00000000 A 0.25363887 0.0673624
hc 1 1.008000 0.00000000 A 0.2600177 0.0870272
DUM_hc 1 0.000000 0.000000 A 0.000000 0.000000
DUM_c3 6 0.000000 0.000000 A 0.000000 0.000000
Na 11 22.99 0.0000 A 2.43928e-01 3.65846e-02
Cl 17 35.45 0.0000 A 4.47766e-01 1.48913e-01
OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00

#include "A-B.itp"

#include "water_and_ions.itp"

[ system ]
; Name
Generic title in water

[ molecules ]
; Compound #mols
A2B 1
SOL 679
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