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Start update of fep examples and doc

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This commit is contained in:
Agilio Padua
2021-01-22 21:39:09 +01:00
parent 70998c0509
commit 25420fc030
9 changed files with 2961 additions and 2644 deletions
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23
examples/USER/fep/CH4hyd/fdti01/fdti01.fep Normal file
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@ -0,0 +1,23 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.000675923 0.998872
200000 0.00676971 0.988725
300000 0.012229 0.979748
400000 0.0195902 0.967815
500000 0.0264713 0.956934
600000 0.0311625 0.949904
700000 0.0149588 0.975649
800000 0.00933401 0.984811
900000 0.00651534 0.989335
1000000 0.00224647 0.996372
1100000 0.00227072 0.996327
1200000 -0.000223228 1.00045
1300000 -0.000553474 1.00099
1400000 -0.00183338 1.00313
1500000 -0.00231784 1.00394
1600000 -0.00338448 1.00572
1700000 -0.00364256 1.00615
1800000 -0.00432816 1.0073
1900000 -0.00528456 1.00891
2000000 -0.00581585 1.00981
2100000 -0.00657668 1.0111

22
examples/USER/fep/CH4hyd/fdti01/fdti01.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.000289416 0.999521
200000 0.00590502 0.990163
300000 0.0115179 0.980934
400000 0.0216052 0.96457
500000 0.0222451 0.963797
600000 0.0200038 0.967603
700000 0.0152292 0.975176
800000 0.00896315 0.985384
900000 0.00585213 0.990434
1000000 0.00327599 0.99467
1100000 0.00159845 0.997437
1200000 0.000171108 0.999804
1300000 -0.000313183 1.00059
1400000 -0.00148 1.00254
1500000 -0.00297976 1.00504
1600000 -0.00287926 1.00487
1700000 -0.00430671 1.00727
1800000 -0.00453729 1.00765
1900000 -0.00507356 1.00856
2000000 -0.00586954 1.0099

14
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp
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@ -72,12 +72,24 @@ compute FEP all fep ${TK} &
atom charge 1 v_dq1 &
atom charge 2 v_dq2
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti01.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti01.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
dump_modify TRAJ element C H O H
run 2000000
unfix ADAPT
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 1.0 # C4H Ow
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # C4H Hw
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 1.0 # H Ow
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # H Hw
set type 1 charge -0.24
set type 2 charge 0.06
run 100000
# write_restart restart.*.lmp
write_data data.*.lmp

5484
examples/USER/fep/CH4hyd/fdti01/log.lammps
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