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Merge branch 'master' into charge_regulation2

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This commit is contained in:
Axel Kohlmeyer
2021-04-12 09:55:15 -04:00
parent 7d95943b7e 9b78426eba
commit e95cbf618b
1731 changed files with 157453 additions and 117722 deletions
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2
examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane
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@ -26,7 +26,7 @@ Masses
7 12.0112
8 1.00797
Pair Coeffs # lj/class2/coul/long
Pair Coeffs # hybrid
1 lj/class2/coul/long 0.054 4.01
2 lj/class2/coul/long 0.054 4.01

4
examples/USER/fep/C7inEthanol/fep01/in.insertion
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@ -12,7 +12,7 @@ improper_style class2
pair_modify mix sixthpower tail yes
special_bonds lj/coul 0 0 1
read_data data.init_conf_without_heptane
read_data data.init_conf_with_heptane
pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 0.0
pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 0.0
@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
atom charge 8 v_q3 &
after yes
thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
thermo_modify line one
thermo 100

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examples/USER/fep/C7inEthanol/fep01/log.insertion Normal file
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examples/USER/fep/C7inEthanol/fep01/log.lammps
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2
examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane
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@ -26,7 +26,7 @@ Masses
7 12.0112
8 1.00797
Pair Coeffs # lj/class2/coul/long
Pair Coeffs # hybrid
1 lj/class2/coul/long 0.054 4.01
2 lj/class2/coul/long 0.054 4.01

2
examples/USER/fep/C7inEthanol/fep10/in.deletion
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@ -47,7 +47,7 @@ fix ADAPT all adapt/fep 10 &
atom charge 8 v_q3 &
after yes
thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
thermo_style custom step temp press vol etotal pe v_lambda v_q1 v_q2 v_q3
thermo_modify line one
thermo 100

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examples/USER/fep/C7inEthanol/fep10/log.lammps
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53
examples/USER/fep/CC-CO/README → examples/USER/fep/CC-CO/README.md
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@ -2,14 +2,14 @@ Ethane to Methanol in Water
===========================
Example calculation of the difference in free energy of hydration upon
transforming ethane into methanol with LAMMPS using *compute fep* and
*fix adapt/fep*.
transforming ethane into methanol with LAMMPS using *compute fep*,
*fix adapt/fep* and *pair lj/cut/coul/long/soft*.
Ethane and methanol are represented by the OPLS-AA force field (1
molecule). Water is represented by the 3-site SPC/E model (360
molecules).
The strategy used to perform the alchemical transformation is the
The procedure used to perform the alchemical transformation is the
following:
* The dual topology approach is used, therefore all the atoms of
@ -18,13 +18,20 @@ following:
transformation. Masses and intramolecular terms (bond lengths,
angles, dihedrals) are not changed.
* Interactions of sites that are being created (from dummy sites) or
deleted (to become dummy sites) are treated using soft-core verions
* Interactions of sites that are being created (from dummy sites, XD-) or
deleted (to become dummy sites, X-D) are treated using soft-core verions
of the Lennard-Jones and Coulomb potentials (*pair
lj/cut/coul/long/soft*) in order to avoid singularities. The
exponent of the coupling parameter lambda in the soft-core pair
potentials was in this example n = 1.
* In order to avoid catastrophic overlaps between the fragments being created
and being deleted, interactions between certain atoms need to be zeroed.
In this case this concerns the H atoms of the methyl group and the O atom
of the OH group involved in the transformation. Other pairs of atoms
belonging to these fragments are either within the 1-2 and 1-3 neighbor
relations, or are H atoms with no LJ site (H of the OH group).
* Eletrostatic charges that are modified are varied linearly from the
initial to the final values. This keeps the overall charge of the
molecule constant, which is good for the long range electrostatics
@ -44,42 +51,20 @@ integration (TI/FDTI) and Bennet's acceptance ratio methods:
* `fep10` -- Calculation using FEP, multi-stage transformation of a
methanol molecule into ethane. Results in `fep10.lmp`
* `fdti01` -- Calculation using FDTI, transformation of an
ethane molecule into methanol. Results in `fdti01.lmp`
* `fdti10` -- Calculation using FDTI, transformation of a
methanol molecule into ethane. Results in `fdti10.lmp`
* `bar01` -- Calculation using BAR, 1-step transformation of an
ethane molecule into methanol. Results in `bar01.lmp`
* `bar10` -- Calculation using BAR, 1-step transformation of a
methanol molecule into ethane. Results in `bar10.lmp`
The free-energy profiles can be observed by plotting the values in the
third column of the results files. The Python scripts `fep.py`,
`nti.py`, `fdti.py`, and `bar.py` found in the `tools` directory can
be used to calculate the free-energy differences corresponding to the
above transformations:
third column of the results files. The Python script `fep.py`, found in
the `tools` directory, can be used to calculate the free-energy differences
corresponding to the above transformations:
fep.py 300 < fep01.lmp
fep.py 300 < fep10.lmp
nti.py 300 0.002 < fdti01.lmp
nti.py 300 0.002 < fdti10.lmp
fdti.py 300 0.002 < fdti01.lmp
fdti.py 300 0.002 < fdti10.lmp
bar.py 300 bar01.lmp bar10.lmp
The outputs are in kcal/mol and can be compared with the experimental
value of -6.93 kcal/mol and with simulation value from the literature:
-6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050], -6.8
kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447].
value of -6.93 kcal/mol and with simulation value from the literature
(obtained with different force field parameters):
-6.7 kcal/mol [Jorgensen, Ravimohan, J Chem Phys 83 (1985) 3050](https://doi.org/10.1063/1.449208),
-6.8 kcal/mol [Goette, Grubmüller, J Comp Chem 30 (2007) 447](https://doi.org/10.1002/jcc.21073).
These example calculations are for tutorial purposes only. The results
may not be of research quality (not enough sampling, size of the step

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examples/USER/fep/CC-CO/bar01/bar01.lmp
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examples/USER/fep/CC-CO/bar01/in.bar01.lmp
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@ -1,120 +0,0 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
run 100000
reset_timestep 0
variable dlambda equal 1.0
variable minusdl equal -1.0
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2 &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
# compute cMSD all msd
# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

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examples/USER/fep/CC-CO/bar01/log.lammps
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examples/USER/fep/CC-CO/bar10/bar10.lmp
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examples/USER/fep/CC-CO/bar10/in.bar10.lmp
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@ -1,120 +0,0 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.1.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # CO-C CO-C
pair_coeff 1 2 none # CO-C CD-
pair_coeff 1 3 none # CO-C HD-
pair_coeff 1 4 none # CO-C H1-H
pair_coeff 1 5 none # CO-C OH-D
pair_coeff 1 6 none # CO-C HO-D
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
pair_coeff 2 2 none # CD- CD-
pair_coeff 2 3 none # CD- HD-
pair_coeff 2 4 none # CD- H1-H
pair_coeff 2 5 none # CD- OH-D
pair_coeff 2 6 none # CD- HO-D
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
pair_coeff 3 3 none # HD- HD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
pair_coeff 3 5 none # HD- OH-D
pair_coeff 3 6 none # HD- HO-D
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
pair_coeff 4 4 none # H1-H H1-H
pair_coeff 4 5 none # H1-H OH-D
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
pair_coeff 5 5 none # OH-D OH-D
pair_coeff 5 6 none # OH-D HO-D
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
pair_coeff 6 6 none # HO-D HO-D
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
run 100000
reset_timestep 0
variable dlambda equal -1.0
variable minusdl equal 1.0
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2 &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar10.lmp
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
# compute cMSD all msd
# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

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examples/USER/fep/CC-CO/fdti01/fdti01.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix fFEP
# TimeStep c_cFEP[1] c_cFEP[2]
125000 0.00871763 0.985497
250000 0.00705519 0.98825
375000 0.00568771 0.99052
500000 0.00429336 0.992842
625000 0.00308675 0.994856
750000 0.00169928 0.997181
875000 0.000144366 0.999789
1000000 -0.00112539 1.00193
1125000 -0.0026842 1.00456
1250000 -0.00474318 1.00805
1375000 -0.00571651 1.0097
1500000 -0.0073978 1.01256
1625000 -0.00966334 1.01644
1750000 -0.011584 1.01972
1875000 -0.0148498 1.02535
2000000 -0.0192874 1.03307
2125000 -0.0257123 1.04433
2250000 -0.035944 1.06249
2375000 -0.046465 1.08144
2500000 -0.0558595 1.09863

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examples/USER/fep/CC-CO/fdti01/in.fdti01.lmp
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@ -1,142 +0,0 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
run 250000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
variable minusl equal 1.0-v_lambda
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
variable q2 equal -0.180*(1.0-v_lambda)
variable q3 equal 0.060*(1.0-v_lambda)
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
variable q5 equal -0.683*v_lambda
variable q6 equal 0.418*v_lambda
fix fADAPT all adapt/fep 125000 &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
atom charge 1 v_q1 &
atom charge 2 v_q2 &
atom charge 3 v_q3 &
atom charge 4 v_q4 &
atom charge 5 v_q5 &
atom charge 6 v_q6 &
after yes
variable dlambda equal 0.002
variable minusdl equal -0.002
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2 &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
compute cMSD all msd
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

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examples/USER/fep/CC-CO/fdti01/log.lammps
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examples/USER/fep/CC-CO/fdti10/fdti10.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix fFEP
# TimeStep c_cFEP[1] c_cFEP[2]
125000 0.0632017 0.899723
250000 0.0561376 0.910429
375000 0.0471384 0.924277
500000 0.0349153 0.943416
625000 0.0244399 0.960071
750000 0.019451 0.968073
875000 0.0134728 0.977767
1000000 0.011723 0.980628
1125000 0.00945656 0.984351
1250000 0.00790634 0.986905
1375000 0.00564311 0.990642
1500000 0.00376572 0.993753
1625000 0.00238483 0.996053
1750000 0.00085649 0.9986
1875000 -0.000515888 1.0009
2000000 -0.00151569 1.00257
2125000 -0.00325174 1.00549
2250000 -0.00472612 1.00798
2375000 -0.00578231 1.00976
2500000 -0.00729864 1.01233

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# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.1.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # CO-C CO-C
pair_coeff 1 2 none # CO-C CD-
pair_coeff 1 3 none # CO-C HD-
pair_coeff 1 4 none # CO-C H1-H
pair_coeff 1 5 none # CO-C OH-D
pair_coeff 1 6 none # CO-C HO-D
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
pair_coeff 2 2 none # CD- CD-
pair_coeff 2 3 none # CD- HD-
pair_coeff 2 4 none # CD- H1-H
pair_coeff 2 5 none # CD- OH-D
pair_coeff 2 6 none # CD- HO-D
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
pair_coeff 3 3 none # HD- HD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
pair_coeff 3 5 none # HD- OH-D
pair_coeff 3 6 none # HD- HO-D
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
pair_coeff 4 4 none # H1-H H1-H
pair_coeff 4 5 none # H1-H OH-D
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
pair_coeff 5 5 none # OH-D OH-D
pair_coeff 5 6 none # OH-D HO-D
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
pair_coeff 6 6 none # HO-D HO-D
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
run 250000
reset_timestep 0
variable lambda equal ramp(1.0,0.0)
variable minusl equal 1.0-v_lambda
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
variable q2 equal -0.180*(1.0-v_lambda)
variable q3 equal 0.060*(1.0-v_lambda)
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
variable q5 equal -0.683*v_lambda
variable q6 equal 0.418*v_lambda
fix fADAPT all adapt/fep 125000 &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
atom charge 1 v_q1 &
atom charge 2 v_q2 &
atom charge 3 v_q3 &
atom charge 4 v_q4 &
atom charge 5 v_q5 &
atom charge 6 v_q6 &
after yes
variable dlambda equal -0.002
variable minusdl equal 0.002
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2 &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
compute cMSD all msd
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

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examples/USER/fep/CC-CO/fdti10/log.lammps
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2275
examples/USER/fep/CC-CO/fep01/data.0.lmp
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22
examples/USER/fep/CC-CO/fep01/fep01.fep Normal file
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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.367224 7226.74 10972.3
200000 0.117221 9775.91 10969.8
300000 0.0327981 10833 10957.1
400000 -0.00682693 11431.4 10973.1
500000 -0.0346601 11895.3 10970.6
600000 -0.047293 12165.7 10994.3
700000 -0.0571432 12366.1 10992.6
800000 -0.0643234 12487.6 10947.9
900000 -0.0673497 12638 10962.3
1000000 -0.0821333 13059.7 10957.9
1100000 -0.0652233 12737.3 10966.8
1200000 -0.10943 13955.7 10961
1300000 -0.105325 13902.4 10950.4
1400000 -0.133363 14687.1 10966.7
1500000 -0.171816 16217.4 10959.1
1600000 -0.271532 19801.5 10980.3
1700000 -0.370116 24272.1 10962.7
1800000 -0.58429 36064.2 10939.8
1900000 -0.899593 63323 10933
2000000 -1.12815 101729 10915.2

22
examples/USER/fep/CC-CO/fep01/fep01.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix fFEP
# TimeStep c_cFEP[1] c_cFEP[2]
125000 0.205889 0.714253
250000 0.164934 0.765732
375000 0.131935 0.809532
500000 0.09771 0.859006
625000 0.0688602 0.903005
750000 0.0356141 0.958919
875000 -0.00180317 1.02349
1000000 -0.0317681 1.08115
1125000 -0.0686221 1.15601
1250000 -0.117495 1.2677
1375000 -0.140627 1.31823
1500000 -0.179791 1.41782
1625000 -0.233651 1.57071
1750000 -0.284345 1.71981
1875000 -0.367527 2.01219
2000000 -0.480496 2.54915
2125000 -0.644218 3.47978
2250000 -0.898797 5.57997
2375000 -1.1516 8.56702
2500000 -1.36364 12.2295

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@ -1,143 +0,0 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 25000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
run 10000
reset_timestep 0
write_restart init.restart
variable lambda equal ramp(0.0,1.0)
variable minusl equal 1.0-v_lambda
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
variable q2 equal -0.180*(1.0-v_lambda)
variable q3 equal 0.060*(1.0-v_lambda)
variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
variable q5 equal -0.683*v_lambda
variable q6 equal 0.418*v_lambda
fix fADAPT all adapt/fep 125000 &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_lambda &
atom charge 1 v_q1 &
atom charge 2 v_q2 &
atom charge 3 v_q3 &
atom charge 4 v_q4 &
atom charge 5 v_q5 &
atom charge 6 v_q6 &
after yes
variable dlambda equal 0.05
variable minusdl equal -0.05
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
pair lj/cut/coul/long/soft lambda 5*6 7*8 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2 &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
compute cMSD all msd
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

131
examples/USER/fep/CC-CO/fep01/in.fep01.lmp
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@ -16,70 +16,67 @@ read_data data.0.lmp
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
kspace_style pppm 1.0e-5
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
# use pair soft for atoms that may overlap
# zero epsilon between appearing and desappearing sites: 2-5 3-5
pair_coeff 1 1 lj/cut/coul/long 0.065999 3.500000 # C-CO C-CO
pair_coeff 1 2 lj/cut/coul/long 0.065999 3.500000 # C-CO C-D
pair_coeff 1 3 lj/cut/coul/long 0.044497 2.958040 # C-CO H-D
pair_coeff 1 4 lj/cut/coul/long 0.044497 2.958040 # C-CO H-H1
pair_coeff 1 5 lj/cut/coul/long 0.105924 3.304542 # C-CO OHD-
pair_coeff 1 6 lj/cut/coul/long 0.000000 1.870829 # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.000000 1.870829 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.101281 3.328551 # C-CO Ow
pair_coeff 2 2 lj/cut/coul/long 0.065999 3.500000 # C-D C-D
pair_coeff 2 3 lj/cut/coul/long 0.044497 2.958040 # C-D H-D
pair_coeff 2 4 lj/cut/coul/long 0.044497 2.958040 # C-D H-H1
pair_coeff 2 5 lj/cut/coul/long 0.000000 3.304542 # C-D OHD-
pair_coeff 2 6 lj/cut/coul/long 0.000000 1.870829 # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.000000 1.870829 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.101281 3.328551 1.0 # C-D Ow
pair_coeff 3 3 lj/cut/coul/long 0.030000 2.500000 # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.030000 2.500000 1.0 # H-D H-H1
pair_coeff 3 5 lj/cut/coul/long 0.000000 2.792848 # H-D OHD-
pair_coeff 3 6 lj/cut/coul/long 0.000000 1.581139 # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.000000 1.581139 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.068284 2.813139 1.0 # H-D Ow
pair_coeff 4 4 lj/cut/coul/long 0.030000 2.500000 # H-H1 H-H1
pair_coeff 4 5 lj/cut/coul/long 0.071414 2.792848 # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.000000 1.581139 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.000000 1.581139 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.068284 2.813139 # H-H1 Ow
pair_coeff 5 5 lj/cut/coul/long 0.170000 3.120000 # OHD- OHD-
pair_coeff 5 6 lj/cut/coul/long 0.000000 1.766352 # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.000000 1.766352 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.162549 3.142668 0.0 # OHD- Ow
pair_coeff 6 6 lj/cut/coul/long 0.000000 1.000000 # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.000000 1.000000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.000000 1.779185 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.000000 1.000000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.000000 1.779185 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.155425 3.165500 # Ow Ow
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 2.0
timestep 1.0
velocity all create ${temp} 12345
velocity all create ${TK} 12345
thermo_style multi
thermo ${nprint}
fix SHAKE all shake 0.0001 20 0 b 2 4 5 a 6
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
thermo_style custom step cpu epair emol etotal temp press density
thermo 1000
run 200000
run 250000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
variable minusl equal 1.0-v_lambda
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
@ -89,7 +86,7 @@ variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
variable q5 equal -0.683*v_lambda
variable q6 equal 0.418*v_lambda
fix fADAPT all adapt/fep 125000 &
fix ADAPT all adapt/fep 100000 &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
@ -102,16 +99,16 @@ fix fADAPT all adapt/fep 125000 &
atom charge 6 v_q6 &
after yes
variable dlambda equal 0.05
variable dlambda equal 0.05
variable minusdl equal -0.05
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable dq1 equal (0.145+0.180)*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq4 equal (0.040-0.060)*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
compute FEP all fep ${TK} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
@ -121,22 +118,18 @@ compute cFEP all fep ${temp} &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
atom charge 6 v_dq6 &
volume yes
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep01.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01.fep
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
thermo_style custom step cpu epair emol etotal temp press density v_lambda
compute cMSD all msd
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C C H H O H H O
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
#restart 20000 restart1.lmp restart2.lmp
# restart ${nrestart} restart.*.lmp
run 2000000
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

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examples/USER/fep/CC-CO/fep01/log.lammps
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examples/USER/fep/CC-CO/fep01/log.reference
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@ -1,285 +0,0 @@
LAMMPS (18 Apr 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438)
2 by 2 by 2 MPI processor grid
reading atoms ...
1090 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
10 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
reading bonds ...
729 bonds
reading angles ...
377 angles
reading dihedrals ...
16 dihedrals
5 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
8 = max # of 1-4 neighbors
9 = max # of special neighbors
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable nprint equal 2500000/500
variable ndump equal ${nsteps}/100
variable ndump equal 2500000/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
thermo 5000
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6
1 = # of size 2 clusters
0 = # of size 3 clusters
2 = # of size 4 clusters
360 = # of frozen angles
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500
fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500
fix fNPT all npt temp 300 300 100 iso 1 ${press} 500
fix fNPT all npt temp 300 300 100 iso 1 1 500
run 250000
PPPM initialization ...
G vector (1/distance) = 0.270213
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0169033
estimated relative force accuracy = 5.09037e-05
using double precision FFTs
3d grid and FFT values/proc = 2744 512
SHAKE stats (type/ave/delta) on step 0
2 1.09 4.99625e-06
4 0.945001 0
5 1 1.58341e-05
6 109.47 0.0012593
Memory usage per processor = 8.38576 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -236.7999 KinEng = 0.0000 Temp = 0.0000
PotEng = -236.7999 E_bond = 0.0000 E_angle = 0.3094
E_dihed = 0.0001 E_impro = 0.0000 E_vdwl = -192.9285
E_coul = 19402.7702 E_long = -19446.9511 Press = 406.6448
Volume = 19438.0383
SHAKE stats (type/ave/delta) on step 5000
2 1.09006 8.6791e-07
4 0.945054 0
5 1.00006 3.8639e-06
6 109.47 0.000376049
---------------- Step 5000 ----- CPU = 16.4963 (sec) ----------------
TotEng = -3314.5713 KinEng = 650.7183 Temp = 300.4163
PotEng = -3965.2896 E_bond = 0.0875 E_angle = 1.4729
E_dihed = 0.4749 E_impro = 0.0000 E_vdwl = 774.1508
E_coul = 14908.3382 E_long = -19649.8139 Press = 358.7253
Volume = 10987.1076
SHAKE stats (type/ave/delta) on step 10000
2 1.08998 2.43077e-07
4 0.944985 0
5 0.999985 4.10972e-06
6 109.47 0.000514527
---------------- Step 10000 ----- CPU = 34.0488 (sec) ----------------
TotEng = -3279.4541 KinEng = 689.4215 Temp = 318.2843
PotEng = -3968.8755 E_bond = 0.2040 E_angle = 1.8441
E_dihed = 0.1574 E_impro = 0.0000 E_vdwl = 703.3180
E_coul = 14976.4466 E_long = -19650.8457 Press = -983.5171
Volume = 10927.3524
SHAKE stats (type/ave/delta) on step 15000
2 1.09002 1.0199e-06
4 0.945017 0
5 1.00002 5.08944e-06
6 109.47 0.00042735
---------------- Step 15000 ----- CPU = 53.1541 (sec) ----------------
TotEng = -3368.2566 KinEng = 686.6827 Temp = 317.0199
PotEng = -4054.9393 E_bond = 0.4514 E_angle = 1.5194
E_dihed = 2.4125 E_impro = 0.0000 E_vdwl = 709.7507
E_coul = 14880.7025 E_long = -19649.7759 Press = -1277.1945
Volume = 10817.2760
SHAKE stats (type/ave/delta) on step 20000
2 1.09005 3.84509e-06
4 0.945044 0
5 1.00005 1.15463e-05
6 109.47 0.000893174
---------------- Step 20000 ----- CPU = 67.0658 (sec) ----------------
TotEng = -3401.0672 KinEng = 639.1818 Temp = 295.0902
PotEng = -4040.2490 E_bond = 0.8254 E_angle = 4.2422
E_dihed = 0.6223 E_impro = 0.0000 E_vdwl = 777.7799
E_coul = 14826.3237 E_long = -19650.0425 Press = -268.5153
Volume = 10911.3140
SHAKE stats (type/ave/delta) on step 25000
2 1.09 3.16085e-06
4 0.945002 0
5 1 6.82105e-06
6 109.47 0.000683982
---------------- Step 25000 ----- CPU = 83.1242 (sec) ----------------
TotEng = -3331.9648 KinEng = 658.5638 Temp = 304.0383
PotEng = -3990.5287 E_bond = 0.0504 E_angle = 4.8757
E_dihed = 0.9548 E_impro = 0.0000 E_vdwl = 742.1312
E_coul = 14907.2989 E_long = -19645.8396 Press = -803.8894
Volume = 11243.5807
SHAKE stats (type/ave/delta) on step 30000
2 1.08995 5.90921e-08
4 0.944954 0
5 0.999952 5.01043e-06
6 109.47 0.000369665
---------------- Step 30000 ----- CPU = 96.1911 (sec) ----------------
TotEng = -3321.5197 KinEng = 681.8132 Temp = 314.7718
PotEng = -4003.3328 E_bond = 0.5162 E_angle = 6.2281
E_dihed = 1.2145 E_impro = 0.0000 E_vdwl = 767.4719
E_coul = 14871.6899 E_long = -19650.4535 Press = 63.7724
Volume = 10913.5775
SHAKE stats (type/ave/delta) on step 35000
2 1.08996 3.93868e-07
4 0.944963 0
5 0.999961 4.01003e-06
6 109.47 0.000492251
---------------- Step 35000 ----- CPU = 111.1547 (sec) ----------------
TotEng = -3376.3100 KinEng = 652.5134 Temp = 301.2450
PotEng = -4028.8234 E_bond = 0.6940 E_angle = 3.8874
E_dihed = 0.6796 E_impro = 0.0000 E_vdwl = 811.7936
E_coul = 14803.9468 E_long = -19649.8247 Press = 957.3673
Volume = 10810.8812
SHAKE stats (type/ave/delta) on step 40000
2 1.08993 1.84911e-06
4 0.944937 0
5 0.999934 4.48159e-06
6 109.47 0.000423379
---------------- Step 40000 ----- CPU = 127.8336 (sec) ----------------
TotEng = -3342.5048 KinEng = 641.0827 Temp = 295.9678
PotEng = -3983.5875 E_bond = 1.4592 E_angle = 3.3579
E_dihed = 0.1250 E_impro = 0.0000 E_vdwl = 714.5090
E_coul = 14945.5914 E_long = -19648.6299 Press = -1146.3509
Volume = 10993.6945
SHAKE stats (type/ave/delta) on step 45000
2 1.09004 2.52413e-06
4 0.945038 0
5 1.00004 7.30752e-06
6 109.47 0.000660905
---------------- Step 45000 ----- CPU = 141.7030 (sec) ----------------
TotEng = -3368.5223 KinEng = 640.7082 Temp = 295.7949
PotEng = -4009.2305 E_bond = 0.0226 E_angle = 2.7492
E_dihed = 0.8929 E_impro = 0.0000 E_vdwl = 820.3025
E_coul = 14817.6347 E_long = -19650.8325 Press = 388.8981
Volume = 11292.9397
SHAKE stats (type/ave/delta) on step 50000
2 1.09006 2.89749e-06
4 0.945051 0
5 1.00006 6.08927e-06
6 109.47 0.000779845
---------------- Step 50000 ----- CPU = 156.2936 (sec) ----------------
TotEng = -3253.6028 KinEng = 683.0893 Temp = 315.3610
PotEng = -3936.6921 E_bond = 0.4303 E_angle = 5.1773
E_dihed = 1.1538 E_impro = 0.0000 E_vdwl = 722.3282
E_coul = 14982.9162 E_long = -19648.6979 Press = -338.7238
Volume = 11230.1507
SHAKE stats (type/ave/delta) on step 55000
2 1.09007 9.95472e-07
4 0.945062 0
5 1.00007 3.93786e-06
6 109.47 0.000436645
---------------- Step 55000 ----- CPU = 176.2674 (sec) ----------------
TotEng = -3332.0820 KinEng = 662.9270 Temp = 306.0527
PotEng = -3995.0090 E_bond = 0.8395 E_angle = 1.9527
E_dihed = 1.0770 E_impro = 0.0000 E_vdwl = 750.6359
E_coul = 14899.3802 E_long = -19648.8943 Press = -498.7755
Volume = 11082.6763
SHAKE stats (type/ave/delta) on step 60000
2 1.09006 7.79087e-08
4 0.945052 1.22125e-15
5 1.00006 3.87615e-06
6 109.47 0.000355506
---------------- Step 60000 ----- CPU = 193.3379 (sec) ----------------
TotEng = -3296.5834 KinEng = 679.6746 Temp = 313.7845
PotEng = -3976.2580 E_bond = 2.4610 E_angle = 2.9231
E_dihed = 0.8719 E_impro = 0.0000 E_vdwl = 803.1348
E_coul = 14863.3163 E_long = -19648.9651 Press = 1009.2429
Volume = 11125.1736
SHAKE stats (type/ave/delta) on step 65000
2 1.09003 1.05995e-06
4 0.945023 1.22125e-15
5 1.00003 4.3471e-06
6 109.47 0.000511365
---------------- Step 65000 ----- CPU = 210.3194 (sec) ----------------
TotEng = -3322.0496 KinEng = 666.5091 Temp = 307.7064
PotEng = -3988.5587 E_bond = 0.8728 E_angle = 5.7476
E_dihed = 0.9783 E_impro = 0.0000 E_vdwl = 743.8165
E_coul = 14910.0426 E_long = -19650.0166 Press = -421.7167
Volume = 10902.5998
SHAKE stats (type/ave/delta) on step 70000
2 1.0901 1.09831e-06
4 0.94509 0
5 1.0001 3.59309e-06
6 109.47 0.000361318
---------------- Step 70000 ----- CPU = 228.7878 (sec) ----------------
TotEng = -3395.7912 KinEng = 667.4514 Temp = 308.1414
PotEng = -4063.2426 E_bond = 0.6965 E_angle = 5.1350
E_dihed

287
examples/USER/fep/CC-CO/fep01/log.reference-omp
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@ -1,287 +0,0 @@
LAMMPS (18 Apr 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100)
using 1 OpenMP thread(s) per MPI task
package omp *
using multi-threaded neighbor list subroutines
prefer double precision OpenMP force kernels
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
dihedral_style opls
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
orthogonal box = (-13.4438 -13.4438 -13.4438) to (13.4438 13.4438 13.4438)
2 by 2 by 2 MPI processor grid
reading atoms ...
1090 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
10 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
reading bonds ...
729 bonds
reading angles ...
377 angles
reading dihedrals ...
16 dihedrals
5 = max # of 1-2 neighbors
4 = max # of 1-3 neighbors
8 = max # of 1-4 neighbors
9 = max # of special neighbors
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CO C-CO
pair_coeff 1 2 none # C-CO C-D
pair_coeff 1 3 none # C-CO H-D
pair_coeff 1 4 none # C-CO H-H1
pair_coeff 1 5 none # C-CO OHD-
pair_coeff 1 6 none # C-CO HOD-
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # C-CO Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # C-CO Ow
pair_coeff 2 2 none # C-D C-D
pair_coeff 2 3 none # C-D H-D
pair_coeff 2 4 none # C-D H-H1
pair_coeff 2 5 none # C-D OHD-
pair_coeff 2 6 none # C-D HOD-
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # C-D Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 1.0 # C-D Ow
pair_coeff 3 3 none # H-D H-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 1.0 # H-D H-H1
pair_coeff 3 5 none # H-D OHD-
pair_coeff 3 6 none # H-D HOD-
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H-D Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 4 4 none # H-H1 H-H1
pair_coeff 4 5 none # H-H1 OHD-
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # H-H1 HOD-
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H-H1 Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H-H1 Ow
pair_coeff 5 5 none # OHD- OHD-
pair_coeff 5 6 none # OHD- HOD-
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # OHD- Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 0.0 # OHD- Ow
pair_coeff 6 6 none # HOD- HOD-
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HOD- Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 0.0 # HOD- Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable nprint equal 2500000/500
variable ndump equal ${nsteps}/100
variable ndump equal 2500000/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
neighbor 2.0 bin
timestep 2.0
# velocity all create ${temp} 12345
thermo_style multi
thermo ${nprint}
thermo 5000
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix fSHAKE all shake 0.0001 20 5000 b 2 4 5 a 6
1 = # of size 2 clusters
0 = # of size 3 clusters
2 = # of size 4 clusters
360 = # of frozen angles
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
fix fNPT all npt temp 300 ${temp} 100 iso ${press} ${press} 500
fix fNPT all npt temp 300 300 100 iso ${press} ${press} 500
fix fNPT all npt temp 300 300 100 iso 1 ${press} 500
fix fNPT all npt temp 300 300 100 iso 1 1 500
run 250000
PPPM initialization ...
G vector (1/distance) = 0.270213
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0169033
estimated relative force accuracy = 5.09037e-05
using double precision FFTs
3d grid and FFT values/proc = 2744 512
Hybrid pair style last /omp style lj/cut/coul/long/soft
Last active /omp style is kspace_style pppm/omp
SHAKE stats (type/ave/delta) on step 0
2 1.09 4.99625e-06
4 0.945001 0
5 1 1.58341e-05
6 109.47 0.0012593
Memory usage per processor = 8.38667 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -236.7999 KinEng = 0.0000 Temp = 0.0000
PotEng = -236.7999 E_bond = 0.0000 E_angle = 0.3094
E_dihed = 0.0001 E_impro = 0.0000 E_vdwl = -192.9285
E_coul = 19402.7702 E_long = -19446.9511 Press = 406.6448
Volume = 19438.0383
SHAKE stats (type/ave/delta) on step 5000
2 1.09009 2.87398e-07
4 0.945079 0
5 1.00008 3.9811e-06
6 109.47 0.000369321
---------------- Step 5000 ----- CPU = 11.8253 (sec) ----------------
TotEng = -3307.2904 KinEng = 658.6061 Temp = 304.0578
PotEng = -3965.8965 E_bond = 0.0083 E_angle = 0.6669
E_dihed = 0.2569 E_impro = 0.0000 E_vdwl = 734.5556
E_coul = 14945.5504 E_long = -19646.9346 Press = -401.3652
Volume = 10990.0279
SHAKE stats (type/ave/delta) on step 10000
2 1.08991 8.10164e-07
4 0.944925 0
5 0.999922 7.76553e-06
6 109.47 0.000694232
---------------- Step 10000 ----- CPU = 23.7032 (sec) ----------------
TotEng = -3381.5340 KinEng = 646.2577 Temp = 298.3570
PotEng = -4027.7917 E_bond = 0.2113 E_angle = 1.2103
E_dihed = 0.8831 E_impro = 0.0000 E_vdwl = 807.4931
E_coul = 14812.7871 E_long = -19650.3766 Press = 1168.7845
Volume = 10591.5096
SHAKE stats (type/ave/delta) on step 15000
2 1.08988 6.96695e-07
4 0.944894 0
5 0.999889 7.87681e-06
6 109.47 0.000849755
---------------- Step 15000 ----- CPU = 37.0159 (sec) ----------------
TotEng = -3391.4919 KinEng = 640.6926 Temp = 295.7878
PotEng = -4032.1845 E_bond = 0.3271 E_angle = 2.4027
E_dihed = 0.2102 E_impro = 0.0000 E_vdwl = 833.3641
E_coul = 14781.8806 E_long = -19650.3692 Press = 1246.1602
Volume = 10806.8631
SHAKE stats (type/ave/delta) on step 20000
2 1.09009 5.35061e-07
4 0.945076 0
5 1.00008 5.8947e-06
6 109.47 0.000481652
---------------- Step 20000 ----- CPU = 49.5427 (sec) ----------------
TotEng = -3340.9663 KinEng = 649.0129 Temp = 299.6290
PotEng = -3989.9791 E_bond = 0.2338 E_angle = 1.4422
E_dihed = 0.7066 E_impro = 0.0000 E_vdwl = 823.4408
E_coul = 14835.4457 E_long = -19651.2482 Press = 1369.0812
Volume = 10984.3808
SHAKE stats (type/ave/delta) on step 25000
2 1.09003 1.29003e-06
4 0.945026 0
5 1.00003 5.08541e-06
6 109.47 0.000543653
---------------- Step 25000 ----- CPU = 61.5352 (sec) ----------------
TotEng = -3350.1301 KinEng = 628.6694 Temp = 290.2370
PotEng = -3978.7994 E_bond = 0.5250 E_angle = 3.3362
E_dihed = 1.1997 E_impro = 0.0000 E_vdwl = 753.6460
E_coul = 14908.8825 E_long = -19646.3890 Press = -107.3383
Volume = 10858.4423
SHAKE stats (type/ave/delta) on step 30000
2 1.09012 2.15723e-06
4 0.945104 0
5 1.00011 7.30223e-06
6 109.47 0.000722195
---------------- Step 30000 ----- CPU = 75.1590 (sec) ----------------
TotEng = -3291.1533 KinEng = 662.9659 Temp = 306.0706
PotEng = -3954.1192 E_bond = 0.0386 E_angle = 3.4541
E_dihed = 0.3158 E_impro = 0.0000 E_vdwl = 745.0479
E_coul = 14947.2099 E_long = -19650.1856 Press = -296.2930
Volume = 11301.5139
SHAKE stats (type/ave/delta) on step 35000
2 1.08998 1.28162e-06
4 0.944981 0
5 0.999982 8.25561e-06
6 109.47 0.000790911
---------------- Step 35000 ----- CPU = 86.8870 (sec) ----------------
TotEng = -3370.6689 KinEng = 637.0075 Temp = 294.0864
PotEng = -4007.6763 E_bond = 0.2585 E_angle = 2.7426
E_dihed = 0.2288 E_impro = 0.0000 E_vdwl = 766.3429
E_coul = 14871.1344 E_long = -19648.3835 Press = -434.1739
Volume = 11077.2342
SHAKE stats (type/ave/delta) on step 40000
2 1.09005 3.30799e-07
4 0.945044 0
5 1.00005 4.39187e-06
6 109.47 0.000367325
---------------- Step 40000 ----- CPU = 102.1257 (sec) ----------------
TotEng = -3318.0442 KinEng = 694.3948 Temp = 320.5803
PotEng = -4012.4390 E_bond = 0.3986 E_angle = 4.3594
E_dihed = 1.0551 E_impro = 0.0000 E_vdwl = 716.6662
E_coul = 14914.0530 E_long = -19648.9712 Press = -1177.4188
Volume = 11087.6184
SHAKE stats (type/ave/delta) on step 45000
2 1.08997 7.63663e-06
4 0.944973 0
5 0.999973 2.30441e-05
6 109.47 0.00155851
---------------- Step 45000 ----- CPU = 119.3648 (sec) ----------------
TotEng = -3371.5332 KinEng = 660.1645 Temp = 304.7773
PotEng = -4031.6977 E_bond = 1.3352 E_angle = 2.6760
E_dihed = 1.0255 E_impro = 0.0000 E_vdwl = 734.4320
E_coul = 14878.0777 E_long = -19649.2440 Press = -978.3955
Volume = 11108.5059
SHAKE stats (type/ave/delta) on step 50000
2 1.09015 1.28872e-06
4 0.945128 0
5 1.00014 5.27234e-06
6 109.47 0.000408939
---------------- Step 50000 ----- CPU = 132.4029 (sec) ----------------
TotEng = -3345.1117 KinEng = 660.2366 Temp = 304.8106
PotEng = -4005.3482 E_bond = 0.9878 E_angle = 3.3427
E_dihed = 0.4740 E_impro = 0.0000 E_vdwl = 763.3350
E_coul = 14874.5886 E_long = -19648.0763 Press = 257.8221
Volume = 10750.8743
SHAKE stats (type/ave/delta) on step 55000
2 1.09006 1.79853e-06
4 0.945055 0
5 1.00006 8.96473e-06
6 109.47 0.000604022
---------------- Step 55000 ----- CPU = 144.3965 (sec) ----------------
TotEng = -3329.0112 KinEng = 639.1918 Temp = 295.0949
PotEng = -3968.2030 E_bond = 0.3779 E_angle = 4.2627
E_dihed = 0.1647 E_impro = 0.0000 E_vdwl = 775.0143
E_coul = 14900.7482 E_long = -19648.7708 Press = 384.3466
Volume = 10943.9465
SHAKE stats (type/ave/delta) on step 60000
2 1.09006 5.76725e-07
4 0.94505 0
5 1.00005 4.15938e-06
6 109.47 0.000456895
---------------- Step 60000 ----- CPU = 158.9285 (sec) ----------------
TotEng = -3337.6373 KinEng = 686.3391 Temp = 316.8613
PotEng = -4023.9764 E_bond = 0.1951 E_angle = 3.2295
E_dihed = 0.2227 E_impro = 0.0000 E_vdwl = 803.8460
E_coul = 14822.5916 E_long = -19654.0613 Press = 343.2839
Volume = 11053.5476
SHAKE stats (type/ave/delta) on step 65000
2 1.08992 1.92627e-06
4 0.944928 0
5 0.999925 9.65284e-06
6 109.47 0.000982037
---------------- Step 65000 ----- CPU = 171.6679 (sec) ----------------
TotEng = -3286.1431 KinEng = 655.6296 Temp = 302.6837
PotEng = -3941.7726 E_bond = 0.8912 E_angle = 5.2439
E_dihed = 1.0392 E_impro = 0.0000 E_vdwl = 723.8338
E_coul = 14977.3056 E_long = -19650.0863 Press = -610.8426
Volume = 11125.9793
SHAKE stats (type/ave/delta) on step 70000
2 1.08995 3.49023e-07
4 0.944954 0
5 0.999952 3.62092e-06
6 109.47 0.000402967
---------------- Step 70000 ----- CPU

22
examples/USER/fep/CC-CO/fep10/fep10.fep Normal file
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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 1.55561 1173.35 10967.2
200000 1.26758 1706.42 10917.2
300000 0.91231 3045.94 10923.2
400000 0.639111 4499.99 10961.2
500000 0.40046 6497.21 10962.2
600000 0.279001 7565.63 10963.9
700000 0.233332 8053.37 10927.2
800000 0.150123 9047.58 10949.7
900000 0.159809 8841.01 10966.4
1000000 0.146608 9019.04 10941.9
1100000 0.121731 9308.38 10929.3
1200000 0.10571 9530.24 10970.7
1300000 0.0851774 9781.09 10983.2
1400000 0.0889958 9711.62 10952.8
1500000 0.0758179 9904.38 10962.1
1600000 0.0687379 10005.4 10953.8
1700000 0.0500615 10342.1 10928
1800000 0.0165215 11146.2 10997
1900000 -0.0358799 12457.9 11003.3
2000000 -0.136771 16018.6 10954

22
examples/USER/fep/CC-CO/fep10/fep10.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix fFEP
# TimeStep c_cFEP[1] c_cFEP[2]
125000 1.6302 0.0823708
250000 1.42237 0.11283
375000 1.1798 0.168088
500000 0.869449 0.279336
625000 0.610803 0.412455
750000 0.489597 0.486584
875000 0.34439 0.601048
1000000 0.303411 0.640696
1125000 0.244627 0.70206
1250000 0.204737 0.746389
1375000 0.144716 0.816302
1500000 0.0941156 0.880968
1625000 0.0575351 0.933564
1750000 0.0171831 0.992497
1875000 -0.018964 1.05078
2000000 -0.0457397 1.09726
2125000 -0.0904898 1.17888
2250000 -0.128205 1.25226
2375000 -0.155891 1.31122
2500000 -0.194237 1.3965

131
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@ -16,70 +16,67 @@ read_data data.1.lmp
pair_style hybrid lj/cut/coul/long 10.0 10.0 &
lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm 1.0e-4
kspace_style pppm 1.0e-5
pair_coeff 1 1 none # CO-C CO-C
pair_coeff 1 2 none # CO-C CD-
pair_coeff 1 3 none # CO-C HD-
pair_coeff 1 4 none # CO-C H1-H
pair_coeff 1 5 none # CO-C OH-D
pair_coeff 1 6 none # CO-C HO-D
pair_coeff 1 7 lj/cut/coul/long 0.0000 1.0000 # CO-C Hw
pair_coeff 1 8 lj/cut/coul/long 0.1013 3.3286 # CO-C Ow
pair_coeff 2 2 none # CD- CD-
pair_coeff 2 3 none # CD- HD-
pair_coeff 2 4 none # CD- H1-H
pair_coeff 2 5 none # CD- OH-D
pair_coeff 2 6 none # CD- HO-D
pair_coeff 2 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # CD- Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.1013 3.3286 0.0 # CD- Ow
pair_coeff 3 3 none # HD- HD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.0300 2.5000 0.0 # HD- H1-H
pair_coeff 3 5 none # HD- OH-D
pair_coeff 3 6 none # HD- HO-D
pair_coeff 3 7 lj/cut/coul/long/soft 0.0000 1.0000 0.0 # HD- Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
pair_coeff 4 4 none # H1-H H1-H
pair_coeff 4 5 none # H1-H OH-D
pair_coeff 4 6 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # H1-H HO-D
pair_coeff 4 7 lj/cut/coul/long 0.0000 1.0000 # H1-H Hw
pair_coeff 4 8 lj/cut/coul/long 0.0683 2.8131 # H1-H Ow
pair_coeff 5 5 none # OH-D OH-D
pair_coeff 5 6 none # OH-D HO-D
pair_coeff 5 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # OH-D Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.1625 3.1427 1.0 # OH-D Ow
pair_coeff 6 6 none # HO-D HO-D
pair_coeff 6 7 lj/cut/coul/long/soft 0.0000 1.0000 1.0 # HO-D Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.0000 1.7792 1.0 # HO-D Ow
pair_coeff 7 7 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.0000 1.0000 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
# use pair soft for atoms that may overlap
# zero epsilon between appearing and desappearing sites: 2-5 3-5
pair_coeff 1 1 lj/cut/coul/long 0.065999 3.500000 # CO-C CO-C
pair_coeff 1 2 lj/cut/coul/long 0.065999 3.500000 # CO-C CD-
pair_coeff 1 3 lj/cut/coul/long 0.044497 2.958040 # CO-C HD-
pair_coeff 1 4 lj/cut/coul/long 0.044497 2.958040 # CO-C H1-H
pair_coeff 1 5 lj/cut/coul/long 0.105924 3.304542 # CO-C OH-D
pair_coeff 1 6 lj/cut/coul/long 0.000000 1.870829 # CO-C HO-D
pair_coeff 1 7 lj/cut/coul/long 0.000000 1.870829 # CO-C Hw
pair_coeff 1 8 lj/cut/coul/long 0.101281 3.328551 # CO-C Ow
pair_coeff 2 2 lj/cut/coul/long 0.065999 3.500000 # CD- CD-
pair_coeff 2 3 lj/cut/coul/long 0.044497 2.958040 # CD- HD-
pair_coeff 2 4 lj/cut/coul/long 0.044497 2.958040 # CD- H1-H
pair_coeff 2 5 lj/cut/coul/long 0.000000 3.304542 # CD- OH-D
pair_coeff 2 6 lj/cut/coul/long 0.000000 1.870829 # CD- HO-D
pair_coeff 2 7 lj/cut/coul/long/soft 0.000000 1.870829 0.0 # CD- Hw
pair_coeff 2 8 lj/cut/coul/long/soft 0.101281 3.328551 0.0 # CD- Ow
pair_coeff 3 3 lj/cut/coul/long 0.030000 2.500000 # HD- HD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.030000 2.500000 0.0 # HD- H1-H
pair_coeff 3 5 lj/cut/coul/long 0.000000 2.792848 # HD- OH-D
pair_coeff 3 6 lj/cut/coul/long 0.000000 1.581139 # HD- HO-D
pair_coeff 3 7 lj/cut/coul/long/soft 0.000000 1.581139 0.0 # HD- Hw
pair_coeff 3 8 lj/cut/coul/long/soft 0.068284 2.813139 0.0 # HD- Ow
pair_coeff 4 4 lj/cut/coul/long 0.030000 2.500000 # H1-H H1-H
pair_coeff 4 5 lj/cut/coul/long 0.071414 2.792848 # H1-H OH-D
pair_coeff 4 6 lj/cut/coul/long/soft 0.000000 1.581139 1.0 # H1-H HO-D
pair_coeff 4 7 lj/cut/coul/long 0.000000 1.581139 # H1-H Hw
pair_coeff 4 8 lj/cut/coul/long 0.068284 2.813139 # H1-H Ow
pair_coeff 5 5 lj/cut/coul/long 0.170000 3.120000 # OH-D OH-D
pair_coeff 5 6 lj/cut/coul/long 0.000000 1.766352 # OH-D HO-D
pair_coeff 5 7 lj/cut/coul/long/soft 0.000000 1.766352 1.0 # OH-D Hw
pair_coeff 5 8 lj/cut/coul/long/soft 0.162549 3.142668 1.0 # OH-D Ow
pair_coeff 6 6 lj/cut/coul/long 0.000000 1.000000 # HO-D HO-D
pair_coeff 6 7 lj/cut/coul/long/soft 0.000000 1.000000 1.0 # HO-D Hw
pair_coeff 6 8 lj/cut/coul/long/soft 0.000000 1.779185 1.0 # HO-D Ow
pair_coeff 7 7 lj/cut/coul/long 0.000000 1.000000 # Hw Hw
pair_coeff 7 8 lj/cut/coul/long 0.000000 1.779185 # Hw Ow
pair_coeff 8 8 lj/cut/coul/long 0.155425 3.165500 # Ow Ow
variable nsteps equal 2500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 2.0
timestep 1.0
velocity all create ${temp} 12345
velocity all create ${TK} 12345
thermo_style multi
thermo ${nprint}
fix SHAKE all shake 0.0001 20 0 b 2 4 5 a 6
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 4 5 a 6
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
thermo_style custom step cpu epair emol etotal temp press density
thermo 1000
run 200000
run 250000
reset_timestep 0
variable lambda equal ramp(1.0,0.0)
variable minusl equal 1.0-v_lambda
variable q1 equal 0.145*v_lambda-0.180*(1.0-v_lambda)
@ -89,7 +86,7 @@ variable q4 equal 0.040*v_lambda+0.060*(1.0-v_lambda)
variable q5 equal -0.683*v_lambda
variable q6 equal 0.418*v_lambda
fix fADAPT all adapt/fep 125000 &
fix ADAPT all adapt/fep 100000 &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusl &
pair lj/cut/coul/long/soft lambda 4 6 v_lambda &
@ -103,15 +100,15 @@ fix fADAPT all adapt/fep 125000 &
after yes
variable dlambda equal -0.05
variable minusdl equal 0.05
variable dq1 equal 0.145*v_dlambda+0.180*v_dlambda
variable minusdl equal 0.05
variable dq1 equal (0.145+0.180)*v_dlambda
variable dq2 equal 0.180*v_dlambda
variable dq3 equal -0.060*v_dlambda
variable dq4 equal 0.040*v_dlambda-0.060*v_dlambda
variable dq4 equal (0.040-0.060)*v_dlambda
variable dq5 equal -0.683*v_dlambda
variable dq6 equal 0.418*v_dlambda
compute cFEP all fep ${temp} &
compute FEP all fep ${TK} &
pair lj/cut/coul/long/soft lambda 2*3 7*8 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4 v_minusdl &
pair lj/cut/coul/long/soft lambda 4 6 v_dlambda &
@ -121,22 +118,18 @@ compute cFEP all fep ${temp} &
atom charge 3 v_dq3 &
atom charge 4 v_dq4 &
atom charge 5 v_dq5 &
atom charge 6 v_dq6
atom charge 6 v_dq6 &
volume yes
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fep10.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10.fep
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
thermo_style custom step cpu epair emol etotal temp press density v_lambda
compute cMSD all msd
fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C C H H O H H O
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C C H H O H H O
#restart 20000 restart1.lmp restart2.lmp
# restart ${nrestart} restart.*.lmp
run 2000000
run ${nsteps}
write_restart restart.*.lmp
write_data data.*.lmp

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@ -1,57 +0,0 @@
Methane to Tetrafluoromethane in Water
======================================
Example calculation of the difference in free energy of hydration upon
transforming methane into tetrafluoromethane with LAMMPS using
*compute fep* and *fix adapt*.
Methane and tetrafluoromethane are represented by the OPLS-AA force
field (1 molecule). Water is represented by the 3-site SPC/E model
(360 molecules).
The strategy used to perform the alchemical transformation is the
following:
* The dual topology approach is used, therefore all the atoms of
methane and perfluorommethane are present throughout the simulation,
only some of them are dummy sites at the endpoints of the
transformation. Masses and intramolecular terms (bond lengths,
angles, dihedrals) are not changed.
* Interactions of sites that are being created (from dummy sites) or
deleted (to become dummy sites) are treated using soft-core verions
of the Lennard-Jones and Coulomb potentials (*pair
lj/cut/coul/long/soft*) in order to avoid singularities. The
exponent of the coupling parameter lambda in the soft-core pair
potentials was in this example n = 1.
* Eletrostatic charges that are modified are varied linearly from the
initial to the final values. This keeps the overall charge of the
molecule constant, which is good for the long range electrostatics
(the coupling parameter lambda has no effect on the kspace terms).
The following directories contain input files and results for
calculations using Bennet's acceptance ratio (BAR) method:
* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
molecule into CF4. Results in `bar01.lmp`
* `bar10` -- Calculation using BAR, 1-step transformation of a
CF4 molecule into CH4. Results in `bar10.lmp`
The Python script `bar.py` found in the `tools` directory can
be used to calculate the free-energy difference corresponding to the
transformation:
bar.py 300 bar01.lmp bar10.lmp
The outputs are in kcal/mol and can be compared with the experimental
value of 1.2 kcal/mol and with a simulation value from the literature
(using a different force field): 0.8 kcal/mol
[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103]. This small
free energy difference is difficult to predict.
These example calculations are for tutorial purposes only. The results
may not be of research quality (not enough sampling, size of the step
in lambda or of the delta for numerical derivative not optimized, no
evaluation of ideal-gas contributions, etc.)

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Methane to Tetrafluoromethane in Water
======================================
Example calculation of the difference in free energy of hydration upon
transforming methane into tetrafluoromethane with LAMMPS using
*compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
Methane and tetrafluoromethane are represented by the OPLS-AA force
field (1 molecule). Water is represented by the 3-site SPC/E model
(360 molecules).
The procedure used to perform the alchemical transformation is the
following:
* The dual topology approach is used, therefore all the atoms of
methane and perfluorommethane are present throughout the simulation,
only some of them are dummy sites at the endpoints of the
transformation. Masses and intramolecular terms (bonds, angles, dihedrals)
are not changed.
* Interactions of sites that are being created (from dummy sites, XD-) or
deleted (to become dummy sites X-D) are treated using soft-core versions
of the Lennard-Jones and Coulomb potentials (*pair
lj/cut/coul/long/soft*) in order to avoid singularities. The
exponent of the coupling parameter lambda in the soft-core pair
potentials was in this example n = 1.
* Atoms of the fragments being created should not interact with atoms being
deleted. In this small solute this is guaranteed by the exclusion of 1-2
and 1-3 interactions, so no modifications of the *pair_coeff* are needed.
Otherwise the LJ epsilon of those interactions should be zeroed.
* Eletrostatic charges that are modified are varied linearly from the
initial to the final values. This keeps the overall charge of the
molecule constant, which is good for the long range electrostatics
(the coupling parameter lambda has no effect on the kspace terms).
The following directories contain input files and results for
calculations using the free-energy perturbation and Bennet's acceptance
ratio (BAR) method:
* `mols` -- molecule description files and force field database used
to create the initial configurations used for the simulations
`data.0.lmp` and `data.1.lmp`
* `fep01` -- Calculation using FEP, 20-step transformation of a CH4
molecule into CF4, constant NpT. Results in `fep01.fep`
* `fep10` -- Calculation using FEP, 20-step transformation of a
CF4 molecule into CH4, constant NpT. Results in `fep10.fep`
* `bar01` -- Calculation using BAR, 1-step transformation of a CH4
molecule into CF4, constant NVT, Results in `bar01.fep`
* `bar10` -- Calculation using BAR, 1-step transformation of a
CF4 molecule into CH4, constant NVT. Results in `bar10.fep`
The Python scripts `fep.py` and `bar.py` found in the `tools` directory
can be used to calculate the free-energy difference corresponding to the
transformation:
fep.py 300 < fep01.fep
fep.py 300 < fep10.fep
bar.py 300 bar01.lmp bar10.lmp
The outputs are in kcal/mol and can be compared with the experimental
value of 1.2 kcal/mol, and also with a simulation value from the literature
using a different force field): 0.8 kcal/mol
[Gough, Pearlman, Kolmann, J Chem Phys 99 (1993) 9103](https://doi.org/10.1063/1.465525).
This is a small free energy difference so consider the absolute discrepancies.
These example calculations are for tutorial purposes only. The results
may not be of research quality (not enough sampling, size of the step
in lambda or of the delta for numerical derivative not optimized, no
evaluation of ideal-gas contributions, etc.)

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examples/USER/fep/CH4-CF4/bar01/in.bar01.lmp
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@ -16,74 +16,63 @@ pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10
pair_modify tail yes
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # C-CF C-CF
pair_coeff 1 2 none # C-CF H-D
pair_coeff 1 3 none # C-CF FD-
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C-CF C-CF
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C-CF H-D
pair_coeff 1 3 lj/cut/coul/long 0.0591 3.2133 # C-CF FD-
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # C-CF Hw
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # C-CF Ow
pair_coeff 2 2 none # H-D H-D
pair_coeff 2 3 none # H-D FD-
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H-D H-D
pair_coeff 2 3 lj/cut/coul/long 0.0399 2.7157 # H-D FD-
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 1.0 # H-D Hw
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 3 3 none # FD- FD-
pair_coeff 3 3 lj/cut/coul/long 0.0530 2.9500 # FD- FD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 0.0 # FD- Hw
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 0.0 # FD- Ow
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 2.0
timestep 1.0
velocity all create ${temp} 12345
velocity all create ${TK} 12345
thermo_style multi
thermo ${nprint}
fix SHAKE all shake 0.0001 20 0 b 3 a 4
fix fSHAKE all shake 0.0001 20 ${nprint} b 3 a 4
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 1000
run 200000
reset_timestep 0
unfix NPT
fix NVT all nvt temp ${TK} ${TK} 100
variable dlambda equal 1.0
variable minusdl equal -1.0
variable dqC equal 0.48*v_dlambda-0.24*(1.0-v_dlambda)
variable dqH equal 0.06*(1.0-v_dlambda)
variable dqC equal (0.48+0.24)*v_dlambda
variable dqH equal -0.06*v_dlambda
variable dqF equal -0.12*v_dlambda
compute cFEP all fep ${temp} &
compute FEP all fep ${TK} &
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
atom charge 1 v_dqC &
atom charge 2 v_dqH &
atom charge 3 v_dqF
fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar01.lmp
fix FEP all ave/time 1 1 100 c_FEP[1] c_FEP[2] file bar01.fep
dump TRAJ all custom 5000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H F H O
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
# compute cMSD all msd
# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C H F H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
run 500000
# write_restart restart.*.lmp
write_data data.*.lmp

978
examples/USER/fep/CH4-CF4/bar01/log.bar01 Normal file
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@ -0,0 +1,978 @@
LAMMPS (29 Oct 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
Reading data file ...
orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
2 by 2 by 3 MPI processor grid
reading atoms ...
1089 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
28 = max angles/atom
reading bonds ...
728 bonds
reading angles ...
388 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
8 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
7 = max # of 1-4 neighbors
8 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail yes
kspace_style pppm 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C-CF C-CF
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C-CF H-D
pair_coeff 1 3 lj/cut/coul/long 0.0591 3.2133 # C-CF FD-
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # C-CF Hw
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # C-CF Ow
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H-D H-D
pair_coeff 2 3 lj/cut/coul/long 0.0399 2.7157 # H-D FD-
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 1.0 # H-D Hw
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 3 3 lj/cut/coul/long 0.0530 2.9500 # FD- FD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 0.0 # FD- Hw
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 0.0 # FD- Ow
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
velocity all create 300 12345
fix SHAKE all shake 0.0001 20 0 b 3 a 4
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
360 = # of frozen angles
find clusters CPU = 0.001 seconds
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix NPT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix NPT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix NPT all npt temp 300 300 100 iso 1 ${PBAR} 500
fix NPT all npt temp 300 300 100 iso 1 1 500
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 1000
run 200000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.27021276
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.016910392
estimated relative force accuracy = 5.0925143e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.37 | 16.38 | 16.39 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 798.08888 972.9364 -174.84752 -201.6326 19449.757 -19423.16 448.35165 1094.5342 19438.038 0.56189244
1000 1.6227639 -3135.9243 629.54322 -3765.4676 732.54113 15141.62 -19640.497 290.10811 -234.59752 13323.595 0.81975524
2000 4.3550149 -3333.4048 628.81546 -3962.2203 771.57676 14914.189 -19648.873 289.77274 -306.28703 11774.436 0.92761017
3000 7.2743737 -3309.7195 677.89703 -3987.6166 757.99659 14902.361 -19649.323 312.39067 383.0691 10832.367 1.0082825
4000 10.112018 -3314.5067 641.13741 -3955.6441 769.70713 14921.613 -19647.838 295.45098 510.27803 10888.206 1.0031117
5000 12.706124 -3371.0779 621.77548 -3992.8534 790.65314 14864.613 -19649.217 286.52855 954.94335 10827.277 1.0087566
6000 15.489237 -3353.7143 662.53154 -4016.2459 744.67602 14889.993 -19652.3 305.30989 -422.11945 10980.311 0.99469738
7000 18.236457 -3360.1226 638.50387 -3998.6265 739.96323 14908.61 -19648.408 294.23739 -397.77334 10917.97 1.0003771
8000 21.113473 -3350.5189 659.78194 -4010.3009 763.57322 14874.976 -19650.722 304.04281 58.154192 10905.304 1.0015389
9000 23.987032 -3396.809 626.60232 -4023.4113 776.04899 14849.476 -19650.05 288.75287 263.83864 10861.498 1.0055783
10000 27.076899 -3394.4848 642.63639 -4037.1212 711.4545 14901.365 -19651.143 296.14175 -1267.145 10904.447 1.0016176
11000 30.184956 -3297.1389 686.72595 -3983.8649 753.45058 14907.57 -19646.446 316.45924 441.31675 10709.186 1.0198802
12000 32.719707 -3411.7157 634.98327 -4046.699 757.47342 14841.968 -19647.665 292.61501 -70.867985 10726.666 1.0182182
13000 35.727222 -3374.9645 634.51906 -4009.4836 715.92455 14921.027 -19648.011 292.40109 -665.68165 10807.776 1.0105767
14000 38.770042 -3438.3513 638.93389 -4077.2852 724.17831 14845.131 -19648.377 294.43555 -1171.5416 10807.455 1.0106067
15000 41.35641 -3365.0228 644.87938 -4009.9021 827.30298 14811.105 -19649.786 297.17537 1095.495 10900.078 1.0020191
16000 44.198681 -3365.6605 640.00578 -4005.6663 733.30864 14911.539 -19651.433 294.9295 -893.58882 11099.467 0.98401905
17000 47.004999 -3412.1185 652.8766 -4064.9951 808.29086 14774.583 -19649.833 300.86067 775.16386 10832.393 1.0082802
18000 49.307934 -3413.1241 642.52146 -4055.6455 779.41048 14813.756 -19650.103 296.08878 239.37739 10770.676 1.0140577
19000 52.516104 -3392.8412 652.52618 -4045.3674 780.92671 14821.147 -19649.131 300.69919 -21.897655 10966.136 0.99598314
20000 55.649319 -3330.7426 663.82659 -3994.5692 737.44583 14915.667 -19651.054 305.90668 -465.12194 10903.468 1.0017076
21000 58.277268 -3329.3496 676.78976 -4006.1393 709.91532 14929.303 -19647.492 311.88041 -877.40985 10982.77 0.99447473
22000 60.472235 -3370.5698 636.53863 -4007.1085 773.13288 14865.407 -19649.07 293.33176 563.27108 10931.735 0.99911745
23000 62.767962 -3349.9273 656.01208 -4005.9394 756.49013 14886.996 -19651.417 302.30557 34.763751 10860.428 1.0056774
24000 65.937963 -3325.3063 672.60215 -3997.9084 760.64327 14886.531 -19647.632 309.95067 -164.43976 10936.076 0.99872082
25000 69.103421 -3358.178 677.71691 -4035.8949 755.15482 14857.343 -19650.872 312.30766 -84.92193 10843.837 1.0072161
26000 71.851329 -3347.382 672.1553 -4019.5373 750.87566 14875.682 -19648.128 309.74474 -450.18098 11156.794 0.97896283
27000 74.118636 -3373.0732 664.42954 -4037.5027 805.42361 14801.784 -19647.775 306.18454 615.21813 11013.134 0.99173282
28000 76.02629 -3405.9581 640.38635 -4046.3444 755.70742 14842.59 -19647.534 295.10488 -682.91397 10977.214 0.99497801
29000 77.94268 -3391.7825 660.70223 -4052.4848 741.10988 14850.358 -19646.019 304.4669 -335.54942 10759.014 1.0151568
30000 79.874011 -3420.3523 619.13732 -4039.4897 748.84158 14856.835 -19647.895 285.31283 -555.95656 10817.844 1.0096362
31000 82.529485 -3418.7423 636.16294 -4054.9052 743.02294 14850.469 -19651.029 293.15863 -960.36278 11038.486 0.98945511
32000 85.405709 -3298.6451 710.74972 -4009.3948 713.81064 14923.742 -19648.983 327.52995 -906.58524 10949.584 0.99748877
33000 88.43898 -3345.6779 666.60707 -4012.285 733.59753 14901.4 -19650.877 307.18799 -612.23666 10913.444 1.000792
34000 91.49661 -3398.4259 651.70407 -4050.13 728.38362 14868.157 -19648.637 300.32034 -949.57274 10826.612 1.0088185
35000 94.396664 -3335.5822 679.38748 -4014.9697 748.94256 14883.767 -19650.181 313.0775 -113.94404 10846.052 1.0070104
36000 96.385906 -3444.994 658.12175 -4103.1157 774.99324 14770.478 -19651.116 303.27776 -101.7667 10635.157 1.0269793
37000 98.378928 -3404.8312 649.64154 -4054.4727 876.87186 14716.949 -19649.753 299.36988 2649.1268 10507.427 1.0394635
38000 101.3117 -3344.8928 655.38456 -4000.2773 719.20801 14926.744 -19649.132 302.0164 -504.44754 10717.894 1.0190516
39000 104.48293 -3352.8954 643.29653 -3996.1919 725.72981 14923.677 -19647.526 296.44595 -585.78876 10905.137 1.0015543
40000 107.62957 -3369.9101 637.39998 -4007.31 746.91058 14895.384 -19651.745 293.72869 26.094236 10776.242 1.0135339
41000 110.73764 -3281.4951 648.37198 -3929.867 726.88832 14990.21 -19649.256 298.78484 122.07948 10811.983 1.0101835
42000 113.89317 -3352.4718 637.776 -3990.2478 698.8244 14953.386 -19645.083 293.90197 -323.99367 10553.334 1.0349419
43000 116.98708 -3417.1937 648.96364 -4066.1573 810.87183 14771.133 -19649.478 299.05749 954.79757 10653.129 1.0252468
44000 120.11947 -3399.018 651.38047 -4050.3985 748.86042 14846.364 -19648.669 300.17122 -128.0086 10720.429 1.0188106
45000 123.18405 -3316.4994 663.83111 -3980.3305 730.84729 14933.283 -19646.334 305.90877 -471.03351 10999.966 0.99292005
46000 126.34266 -3379.5773 634.41148 -4013.9888 726.68572 14907.788 -19650.575 292.35152 -362.34441 10704.492 1.0203274
47000 129.39545 -3299.3383 678.74581 -3978.0841 808.75365 14860.115 -19650.314 312.7818 1105.5628 11016.741 0.99140817
48000 132.36242 -3328.0267 663.94989 -3991.9766 738.84 14918.287 -19651.128 305.9635 -149.85725 10954.863 0.99700805
49000 135.4771 -3393.8602 664.10659 -4057.9668 778.728 14808.309 -19648.368 306.03571 367.98933 10714.776 1.0193482
50000 138.67527 -3327.2702 665.60161 -3992.8718 730.52205 14921.662 -19649.656 306.72465 -507.98309 10972.496 0.99540583
51000 141.78402 -3408.9553 647.78836 -4056.7436 800.11595 14792.953 -19651.622 298.5159 733.58442 10770.401 1.0140836
52000 144.97759 -3346.0292 674.59159 -4020.6208 741.7902 14885.791 -19651.2 310.86744 -253.31211 10771.224 1.0140061
53000 148.10596 -3403.6702 647.30126 -4050.9714 702.44537 14892.703 -19650.153 298.29142 -1455.3963 10887.242 1.0032006
54000 151.27561 -3402.2708 635.30832 -4037.5791 784.06045 14824.2 -19649.122 292.7648 456.18379 10895.154 1.002472
55000 154.31059 -3356.8544 658.92367 -4015.7781 763.9178 14867.309 -19649.791 303.6473 383.12741 10764.652 1.0146252
56000 157.35988 -3367.0719 647.68934 -4014.7613 795.24439 14836.387 -19650.473 298.47026 629.99251 10898.792 1.0021374
57000 160.41422 -3331.368 668.9516 -4000.3196 755.42796 14890.939 -19649.119 308.2684 197.64025 10828.027 1.0086867
58000 163.43492 -3419.3941 603.03817 -4022.4323 770.31208 14856.552 -19652.191 277.89397 193.13804 10905.861 1.0014878
59000 166.48169 -3443.906 615.62832 -4059.5343 830.66206 14753.628 -19646.219 283.6958 746.99913 10943.948 0.9980024
60000 169.36167 -3352.4508 639.91257 -3992.3633 756.76722 14897.558 -19648.528 294.88655 -351.80447 11091.83 0.98469655
61000 172.15329 -3332.3304 654.29338 -3986.6238 738.23788 14921.388 -19648.685 301.51356 -412.09881 11155.118 0.97910992
62000 175.18581 -3318.3617 659.16412 -3977.5258 743.21533 14926.246 -19649.542 303.75811 -249.54472 10898.661 1.0021494
63000 178.33253 -3311.1132 642.26966 -3953.3829 723.58338 14967.469 -19647.287 295.97275 -385.33656 10884.406 1.0034619
64000 181.60183 -3383.0314 629.93214 -4012.9636 730.04342 14904.941 -19649.613 290.28733 -969.93156 11056.015 0.9878864
65000 184.69713 -3308.2098 674.52711 -3982.737 747.85911 14913.345 -19646.694 310.83773 -165.84809 11111.7 0.98293571
66000 187.65407 -3364.2868 652.0621 -4016.3489 799.42941 14832.934 -19650.75 300.48533 917.61356 10805.021 1.0108344
67000 190.77911 -3363.9885 638.70705 -4002.6955 761.21697 14884.338 -19650.305 294.33102 635.45937 10546.969 1.0355664
68000 193.86146 -3334.0791 636.44049 -3970.5196 739.73877 14937.166 -19649.614 293.28653 68.912387 10726.537 1.0182304
69000 196.94314 -3418.4919 634.00423 -4052.4961 820.51179 14773.769 -19648.83 292.16385 747.20053 10922.388 0.99997246
70000 199.80403 -3373.947 631.42486 -4005.3719 711.02529 14931.736 -19650.858 290.97521 -1000.4585 11049.818 0.98844045
71000 202.92351 -3343.3809 681.76184 -4025.1427 710.22237 14909.644 -19648.07 314.17166 -1169.1237 10925.148 0.99971979
72000 206.16718 -3370.6387 671.8063 -4042.445 809.06517 14794.279 -19647.383 309.58392 1029.3304 10718.336 1.0190096
73000 209.25575 -3363.0344 648.99348 -4012.0279 752.87791 14883.425 -19650.369 299.07124 -86.557401 10803.898 1.0109394
74000 212.34845 -3344.0362 656.35024 -4000.3864 765.46402 14883.809 -19650.893 302.46141 811.73493 10654.411 1.0251235
75000 215.42493 -3441.0221 643.37193 -4084.394 747.00535 14815.788 -19648.971 296.4807 -687.99101 10758.163 1.0152371
76000 218.18937 -3368.2667 659.91054 -4028.1772 714.27352 14902.671 -19647.297 304.10208 -1093.9805 10977.453 0.99495638
77000 220.42222 -3358.7851 646.86982 -4005.6549 760.48103 14880.703 -19648.521 298.09261 -42.803257 11010.743 0.99194822
78000 222.87324 -3405.3542 646.26899 -4051.6232 751.04556 14847.343 -19651.631 297.81573 -366.845 10836.053 1.0079396
79000 225.85253 -3334.737 652.95347 -3987.6905 773.64001 14886.896 -19649.86 300.8961 739.14565 10643.412 1.0261828
80000 228.94092 -3364.4996 635.46853 -3999.9681 746.74747 14902.651 -19651.381 292.83863 27.34912 10632.941 1.0271934
81000 232.12064 -3336.9105 626.37349 -3963.284 718.41756 14965.831 -19649.999 288.64743 -482.82365 10903.607 1.0016949
82000 235.20638 -3294.8229 639.79024 -3934.6131 765.39251 14946.022 -19647.838 294.83018 937.00266 10804.659 1.0108683
83000 238.13385 -3353.1695 650.04806 -4003.2176 770.82681 14873.109 -19648.497 299.55722 723.14608 10699.458 1.0208075
84000 241.13583 -3401.9404 636.42544 -4038.3659 756.6727 14852.968 -19650.268 293.2796 42.460588 10803.51 1.0109758
85000 243.33306 -3367.905 640.1287 -4008.0337 734.92136 14906.233 -19651.455 294.98614 83.80666 10584.659 1.0318789
86000 245.97371 -3392.4387 646.2809 -4038.7196 806.8106 14801.83 -19649.186 297.82122 438.85782 11015.687 0.99150301
87000 248.12829 -3384.7716 651.77287 -4036.5445 813.19595 14799.513 -19650.99 300.35205 798.80286 10880.565 1.0038162
88000 250.0307 -3377.3051 657.90541 -4035.2105 821.94479 14791.328 -19650.478 303.17806 901.78308 10815.707 1.0098357
89000 251.99639 -3342.4027 670.73846 -4013.1412 804.18895 14822.309 -19644.383 309.09183 1284.3841 10671.02 1.0235279
90000 254.19997 -3420.2163 615.64957 -4035.8659 754.92363 14856.769 -19652.088 283.70559 -269.37533 10945.889 0.99782546
91000 256.93525 -3328.1675 659.51188 -3987.6793 795.80348 14860.244 -19647.865 303.91836 215.60569 11260.45 0.96995114
92000 259.66669 -3358.2213 656.90946 -4015.1307 801.52461 14825.995 -19648.965 302.71911 793.31406 10837.102 1.0078421
93000 262.49811 -3373.1305 631.19068 -4004.3212 743.90076 14898.618 -19650.669 290.8673 -244.18726 10934.883 0.99882981
94000 265.27422 -3417.4348 620.68383 -4038.1186 729.51892 14876.758 -19648.529 286.0255 -988.8428 10948.711 0.99756826
95000 268.02755 -3360.5218 637.85203 -3998.3738 720.68596 14925.393 -19650.463 293.937 14.71448 10617.634 1.0286742
96000 271.08994 -3314.0216 657.16917 -3971.1908 736.14127 14936.736 -19647.832 302.83879 254.74282 10664.142 1.0241881
97000 274.29641 -3347.2386 654.74153 -4001.9801 737.48065 14906.209 -19650.784 301.72007 -392.11361 10859.047 1.0058053
98000 277.5295 -3399.6443 645.62027 -4045.2646 805.86756 14795.989 -19650.991 297.51679 622.88014 10815.931 1.0098148
99000 280.69542 -3409.0821 632.97743 -4042.0595 764.60187 14841.751 -19652.313 291.69067 -26.842273 10728.354 1.018058
100000 283.8378 -3339.8374 658.30631 -3998.1437 761.06109 14888.636 -19652.093 303.36281 -6.0703178 11090.189 0.98484226
101000 286.87721 -3362.1186 661.94979 -4024.0684 742.99972 14878.86 -19649.336 305.04181 -563.29767 11014.995 0.99156528
102000 290.07789 -3386.5733 606.90665 -3993.48 772.90614 14877.66 -19648.487 279.67666 364.80743 10858.193 1.0058843
103000 293.29033 -3324.9554 659.76653 -3984.7219 769.15339 14889.287 -19646.675 304.03571 513.48317 10953.61 0.99712208
104000 296.5465 -3397.1866 620.62139 -4017.808 795.9375 14828.662 -19647.968 285.99672 907.0442 10837.588 1.0077968
105000 299.6883 -3382.4995 648.25877 -4030.7583 797.25655 14816.713 -19649.467 298.73267 412.87326 10959.672 0.99657057
106000 302.8692 -3333.7645 678.18678 -4011.9513 751.75647 14880.712 -19650.503 312.52419 -346.13564 11128.759 0.98142904
107000 305.9912 -3354.9009 648.70234 -4003.6033 814.22481 14828.018 -19651.832 298.93708 1326.7249 10804.094 1.0109212
108000 309.1072 -3323.7826 676.27053 -4000.0531 757.66342 14883.633 -19647.48 311.64114 -14.394857 10890.887 1.0028648
109000 312.30662 -3355.5416 654.20276 -4009.7444 784.10263 14849.23 -19649.707 301.4718 1187.0686 10639.679 1.0265429
110000 315.47373 -3380.3752 631.31939 -4011.6946 745.60134 14883.493 -19646.482 290.92661 -48.374809 10795.436 1.0117319
111000 318.59032 -3401.8334 638.94498 -4040.7784 766.96923 14836.431 -19649.555 294.44066 -354.50407 11003.022 0.99264426
112000 321.59996 -3413.5057 662.60937 -4076.1151 819.41803 14749.595 -19649.635 305.34576 659.18933 10854.637 1.0062139
113000 324.67915 -3370.1107 632.33094 -4002.4416 772.99396 14868.719 -19650.231 291.39276 515.02396 10717.486 1.0190904
114000 327.87951 -3354.0328 673.83429 -4027.8671 812.63712 14801.595 -19648.243 310.51846 985.88879 10790.828 1.012164
115000 331.09494 -3270.8582 652.33372 -3923.192 709.91663 15011.308 -19648.42 300.6105 -514.77178 11022.22 0.99091535
116000 334.36494 -3326.0255 649.26272 -3975.2882 765.32922 14904.188 -19650.521 299.19531 89.704998 11030.013 0.99021519
117000 337.60043 -3314.6976 690.48407 -4005.1817 739.31178 14898.625 -19648.293 318.19107 -706.01302 11136.645 0.98073407
118000 340.73023 -3395.3039 646.25987 -4041.5638 782.89725 14821.981 -19650.706 297.81153 469.89183 10725.427 1.0183358
119000 343.85716 -3352.8785 648.9704 -4001.8489 743.77601 14896.931 -19649.255 299.06061 -72.754473 10827.626 1.0087241
120000 347.02799 -3376.287 646.47293 -4022.7599 780.16074 14841.24 -19649.425 297.90972 677.92401 10559.084 1.0343783
121000 350.14087 -3334.2648 653.54886 -3987.8137 807.03694 14847.086 -19647.143 301.17047 1231.7405 10834.347 1.0080983
122000 353.2703 -3392.1736 659.25807 -4051.4317 790.08415 14802.976 -19648.342 303.8014 608.48434 10755.876 1.015453
123000 356.50134 -3351.3844 661.13084 -4012.5152 765.68373 14865.89 -19647.859 304.66442 455.96449 10769.393 1.0141785
124000 359.75143 -3399.7389 645.59268 -4045.3316 838.17932 14758.228 -19646.284 297.50407 1366.4127 10766.994 1.0144045
125000 362.99561 -3377.9557 642.40716 -4020.3629 764.85444 14856.98 -19648.707 296.03611 50.832713 10833.286 1.008197
126000 366.34009 -3430.9334 620.76964 -4051.703 819.17048 14776.823 -19651.21 286.06504 786.80724 10959.845 0.99655482
127000 369.65576 -3304.0337 657.36979 -3961.4035 722.09865 14961.098 -19650.383 302.93124 -617.63058 11002.927 0.99265288
128000 372.89106 -3350.4912 650.11432 -4000.6055 730.81891 14911.363 -19647.549 299.58775 -345.07238 10848.892 1.0067467
129000 375.9395 -3352.3377 659.05496 -4011.3927 801.5679 14827.902 -19648.553 303.7078 1024.8803 10761.064 1.0149634
130000 379.05924 -3331.3316 646.16758 -3977.4992 702.45572 14961.396 -19648.868 297.769 -813.36433 10734.344 1.0174899
131000 382.24409 -3378.3014 654.56592 -4032.8673 783.17916 14827.183 -19646.825 301.63915 314.88338 10797.279 1.0115592
132000 385.44093 -3294.3184 685.17163 -3979.4901 648.96238 15017.565 -19650.224 315.74297 -2184.2676 11184.021 0.97657963
133000 388.68642 -3343.5645 683.09706 -4026.6615 735.6572 14883.576 -19651.4 314.78696 -1185.4466 10996.315 0.99324975
134000 391.61811 -3362.5165 663.41639 -4025.9329 723.85251 14894.769 -19650.647 305.71765 -1275.2595 11191.14 0.97595841
135000 394.67542 -3415.5801 631.64607 -4047.2262 737.9634 14860.936 -19650.533 291.07715 -1173.4651 10946.547 0.99776548
136000 397.86076 -3387.9696 642.28653 -4030.2562 803.92941 14810.291 -19649.027 295.98052 558.5236 10880.977 1.0037781
137000 400.95476 -3306.5591 669.23431 -3975.7934 765.46865 14899.052 -19648.694 308.39869 -144.69146 11093.497 0.98454859
138000 404.0148 -3436.8724 604.66442 -4041.5368 827.0866 14774.497 -19649.223 278.64338 1039.4942 10877.528 1.0040964
139000 406.90658 -3316.7286 642.07761 -3958.8062 770.14988 14910.151 -19647.123 295.88425 586.61636 10830.229 1.0084817
140000 410.139 -3435.4909 646.60473 -4082.0956 742.88993 14819.762 -19649.242 297.97045 -924.6196 10763.567 1.0147274
141000 412.97397 -3349.8621 665.88867 -4015.7508 824.0151 14802.572 -19649.88 306.85693 1437.0343 10815.766 1.0098301
142000 415.69334 -3389.4803 656.80813 -4046.2884 815.9995 14783.418 -19649.538 302.67241 618.52893 10888.803 1.0030567
143000 418.35581 -3353.9126 657.39556 -4011.3081 754.07514 14876.046 -19648.455 302.94312 -761.67008 11210.215 0.97429771
144000 421.09581 -3399.1395 648.34596 -4047.4854 757.3745 14842.47 -19650.302 298.77285 -290.76144 10918.994 1.0002832
145000 423.89736 -3321.4046 672.82697 -3994.2315 727.01005 14923.103 -19648.023 310.05426 -94.548607 10776.144 1.0135431
146000 426.88246 -3334.4314 646.05182 -3980.4832 718.68787 14945.962 -19650.513 297.71566 -765.92932 10954.651 0.99702734
147000 429.03205 -3354.2563 655.47531 -4009.7316 732.63749 14902.593 -19649.108 302.05822 -430.8045 10725.851 1.0182956
148000 431.18588 -3337.8871 654.61295 -3992.5 769.42856 14880.899 -19650.086 301.66082 755.7811 10683.384 1.0223434
149000 434.07276 -3376.242 641.83503 -4018.0771 774.77423 14853.885 -19649.601 295.77246 361.77483 10814.831 1.0099174
150000 437.03956 -3361.8006 636.53661 -3998.3372 794.62666 14850.839 -19648.304 293.33083 621.45504 10840.943 1.0074849
151000 439.38767 -3385.8031 660.1222 -4045.9253 787.26849 14814.229 -19650.391 304.19961 540.19133 10758.994 1.0151587
152000 442.26277 -3343.2856 669.2682 -4012.5538 753.90842 14877.678 -19648.544 308.4143 -75.500409 10842.74 1.007318
153000 445.11162 -3302.9056 655.9137 -3958.8193 727.60445 14959.349 -19649.544 302.26024 -542.06617 11257.085 0.97024109
154000 447.79634 -3364.4801 640.01767 -4004.4977 786.40365 14853.443 -19648.083 294.93498 167.89008 11070.961 0.98655272
155000 450.80494 -3381.1697 648.14661 -4029.3163 745.34994 14870.872 -19649.681 298.68099 -484.22067 10953.454 0.99713629
156000 453.78255 -3355.8323 690.06687 -4045.8991 801.03438 14796.077 -19647.031 317.99881 646.55058 10808.799 1.010481
157000 456.74023 -3358.0471 624.66039 -3982.7075 751.73555 14908.971 -19646.858 287.85799 -171.8557 10800.265 1.0112796
158000 459.95793 -3361.8345 615.05113 -3976.8857 756.69986 14910.547 -19648.063 283.42982 565.78305 10581.632 1.0321741
159000 463.07595 -3354.6895 650.23744 -4004.9269 814.77489 14825.419 -19649.058 299.64448 1870.0288 10539.543 1.0362961
160000 465.61057 -3387.3316 642.27094 -4029.6026 756.42682 14859.059 -19648.66 295.97334 -306.78395 10898.921 1.0021255
161000 468.44261 -3343.0814 653.61712 -3996.6986 800.28065 14847.812 -19647.964 301.20192 595.15208 11010.736 0.99194886
162000 470.7058 -3324.2673 657.09555 -3981.3628 792.19065 14870.232 -19648.33 302.80486 1199.9282 10744.365 1.016541
163000 473.09732 -3342.7775 679.83215 -4022.6096 727.18841 14897.208 -19650.549 313.28241 -997.06935 11210.914 0.97423699
164000 475.81005 -3379.4848 625.20354 -4004.6883 757.14884 14881.551 -19648.134 288.10828 -76.040761 11090.621 0.9848039
165000 478.15052 -3386.1281 628.34429 -4014.4724 734.93844 14895.393 -19648.215 289.55562 -464.67688 11010.29 0.99198902
166000 480.8469 -3424.9866 658.25206 -4083.2387 818.88571 14746.189 -19651.579 303.33781 614.68026 10849.995 1.0066444
167000 483.26895 -3302.9751 671.15602 -3974.1311 685.34376 14987.713 -19650.202 309.28425 -1418.9099 11021.782 0.99095467
168000 485.209 -3327.7241 643.48556 -3971.2097 721.1792 14953.493 -19648.175 296.53306 -446.08256 10937.132 0.99862443
169000 487.10676 -3431.0038 640.85754 -4071.8613 803.41985 14771.642 -19650.096 295.32201 376.19715 10859.958 1.0057209
170000 489.25367 -3392.2951 632.96022 -4025.2553 780.55886 14838.676 -19647.453 291.68274 56.696342 10877.572 1.0040923
171000 492.07922 -3345.5847 636.41469 -3981.9994 714.60203 14949.089 -19649.18 293.27464 -1535.0279 11266.565 0.96942474
172000 494.84722 -3412.7904 624.36129 -4037.1517 797.10144 14813.176 -19649.883 287.72016 770.10845 10813.91 1.0100035
173000 497.32327 -3332.2803 635.28695 -3967.5672 704.08272 14974.011 -19650.007 292.75495 -1081.8724 11342.367 0.96294601
174000 499.19226 -3372.3767 600.06605 -3972.4427 711.3376 14958.707 -19647.835 276.52435 -963.09077 11005.88 0.99238652
175000 501.11676 -3378.6046 669.43573 -4048.0404 769.70451 14830.409 -19650.915 308.4915 -171.35864 10854.568 1.0062203
176000 503.01936 -3394.9346 634.14852 -4029.0831 693.23185 14923.391 -19648.477 292.23034 -1420.7325 10872.075 1.0046
177000 505.06396 -3411.4372 652.44563 -4063.8828 816.49405 14765.108 -19649.331 300.66207 808.65833 10842.157 1.0073721
178000 508.26742 -3366.5327 658.07457 -4024.6072 737.87074 14884.423 -19650.094 303.25602 -491.38544 11016.79 0.99140371
179000 511.57476 -3434.1251 629.75987 -4063.885 773.094 14804.889 -19647.271 290.20795 -650.98858 10960.219 0.99652083
180000 514.70512 -3383.3969 679.47789 -4062.8748 791.28905 14794.776 -19652.651 313.11917 390.13227 10803.493 1.0109774
181000 517.97242 -3388.246 636.14319 -4024.3892 823.56405 14798.147 -19650.585 293.14953 1415.4269 10861.759 1.0055541
182000 521.23139 -3408.0717 650.85109 -4058.9228 787.82137 14799.668 -19650.028 299.92727 -53.738357 10976.988 0.99499849
183000 524.54272 -3340.7676 643.08656 -3983.8542 743.8686 14917.46 -19648.747 296.3492 -242.82649 11011.924 0.99184185
184000 527.74844 -3433.1964 607.55441 -4040.7509 760.56557 14846.307 -19651.15 279.97516 -197.28739 10818.803 1.0095467
185000 530.94582 -3401.7191 644.98431 -4046.7034 753.52973 14846.192 -19648.963 297.22372 13.718959 10734.268 1.0174971
186000 534.12608 -3423.214 645.14548 -4068.3595 824.69067 14753.103 -19649.007 297.298 897.60049 10756.426 1.0154011
187000 537.23581 -3344.7412 649.84528 -3994.5864 752.1529 14901.88 -19652.455 299.46377 -316.55785 10904.143 1.0016456
188000 539.86768 -3324.6336 669.85221 -3994.4858 782.33881 14869.239 -19648.467 308.68343 344.3233 10934.187 0.99889334
189000 542.81487 -3337.352 659.23929 -3996.5913 737.23792 14910.279 -19647.745 303.79275 -427.15321 11004.478 0.99251298
190000 545.85026 -3408.1123 677.18274 -4085.295 814.76646 14747.084 -19649.094 312.0615 265.85399 10972.917 0.99536771
191000 548.22635 -3374.5792 652.43146 -4027.0106 798.72937 14819.149 -19648.559 300.65554 589.27577 10894.944 1.0024913
192000 550.15801 -3380.4072 663.81497 -4044.2222 764.97864 14837.259 -19648.504 305.90133 24.769315 10859.15 1.0057958
193000 552.10156 -3333.7718 665.59132 -3999.3631 777.8822 14869.312 -19650.441 306.71991 341.07365 10920.172 1.0001753
194000 554.11349 -3353.0683 659.14773 -4012.2161 728.41507 14904.858 -19649.309 303.75055 -526.17181 10900.056 1.0020212
195000 556.0744 -3353.3614 680.88951 -4034.2509 733.19005 14881.482 -19651.024 313.76967 -818.00122 10917.711 1.0004008
196000 558.79417 -3344.6073 652.72643 -3997.3337 746.06025 14902.023 -19648.103 300.79147 -542.4291 10965.793 0.99601433
197000 561.88103 -3361.3955 649.81715 -4011.2127 778.20383 14857.622 -19650.459 299.45081 758.15369 10855.892 1.0060976
198000 564.71123 -3375.0547 639.90978 -4014.9644 769.46044 14864.345 -19651.635 294.88526 541.36956 10764.059 1.0146811
199000 566.62662 -3340.6462 680.56676 -4021.2129 742.41536 14883.325 -19650.541 313.62094 -242.81889 10781.093 1.0130778
200000 568.5192 -3392.5132 655.59989 -4048.1131 788.37821 14810.426 -19650.31 302.11563 452.50967 10884.769 1.0034285
Loop time of 568.519 on 12 procs for 200000 steps with 1089 atoms
Performance: 30.395 ns/day, 0.790 hours/ns, 351.791 timesteps/s
93.1% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 225.29 | 244.44 | 283.93 | 111.9 | 43.00
Bond | 0.13517 | 0.2753 | 1.2102 | 54.4 | 0.05
Kspace | 121.44 | 161.43 | 181.09 | 137.9 | 28.40
Neigh | 20.445 | 20.505 | 20.539 | 0.7 | 3.61
Comm | 53.62 | 59.557 | 62.217 | 42.3 | 10.48
Output | 0.012041 | 0.012435 | 0.016413 | 1.1 | 0.00
Modify | 57.983 | 65.646 | 81.081 | 108.2 | 11.55
Other | | 16.66 | | | 2.93
Nlocal: 90.7500 ave 101 max 83 min
Histogram: 3 1 1 2 0 1 0 1 1 2
Nghost: 3759.42 ave 3809 max 3712 min
Histogram: 2 0 0 3 2 1 1 0 2 1
Neighs: 32260.6 ave 36917 max 28405 min
Histogram: 1 1 2 4 0 0 1 1 0 2
Total # of neighbors = 387127
Ave neighs/atom = 355.48852
Ave special neighs/atom = 2.0495868
Neighbor list builds = 8468
Dangerous builds = 4
reset_timestep 0
unfix NPT
fix NVT all nvt temp ${TK} ${TK} 100
fix NVT all nvt temp 300 ${TK} 100
fix NVT all nvt temp 300 300 100
variable dlambda equal 1.0
variable minusdl equal -1.0
variable dqC equal (0.48+0.24)*v_dlambda
variable dqH equal -0.06*v_dlambda
variable dqF equal -0.12*v_dlambda
compute FEP all fep ${TK} pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda atom charge 1 v_dqC atom charge 2 v_dqH atom charge 3 v_dqF
compute FEP all fep 300 pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda atom charge 1 v_dqC atom charge 2 v_dqH atom charge 3 v_dqF
fix FEP all ave/time 1 1 100 c_FEP[1] c_FEP[2] file bar01.fep
dump TRAJ all custom 5000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H F H O
run 500000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.26771633
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.025848288
estimated relative force accuracy = 7.7841351e-05
using double precision FFTW3
3d grid and FFT values/proc = 1859 144
FEP settings ...
temperature = 300.000000
tail no
lj/cut/coul/long/soft lambda 2-2 4-5
lj/cut/coul/long/soft lambda 3-3 4-5
1-1 charge
2-2 charge
3-3 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.62 | 17.63 | 17.63 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 -3392.5233 655.59989 -4048.1232 788.37821 14629.081 -19468.975 302.11563 66.207268 10884.769 1.0034285
1000 1.6811173 -3299.5075 692.20562 -3991.7131 778.25752 14691.657 -19467.153 318.9844 531.54794 10884.769 1.0034285
2000 3.4266793 -3345.8401 672.15357 -4017.9937 754.89913 14692.39 -19468.044 309.74395 -147.16589 10884.769 1.0034285
3000 5.6563153 -3347.3876 680.24737 -4027.635 801.32207 14634.959 -19469.614 313.47376 608.24729 10884.769 1.0034285
4000 8.3285509 -3422.8843 642.07627 -4064.9605 749.54977 14646.739 -19465.434 295.88363 -798.2545 10884.769 1.0034285
5000 11.003447 -3395.7269 651.90953 -4047.6364 794.41883 14625.696 -19470.699 300.41502 424.90838 10884.769 1.0034285
6000 13.554516 -3379.3207 658.82739 -4038.1481 774.56484 14650.196 -19467.307 303.60294 264.50083 10884.769 1.0034285
7000 16.06654 -3328.1712 672.06632 -4000.2376 770.43733 14691.469 -19467.518 309.70374 374.91512 10884.769 1.0034285
8000 18.586977 -3346.4967 669.43289 -4015.9296 713.43009 14734.686 -19468.413 308.49019 -994.22271 10884.769 1.0034285
9000 21.139807 -3421.4727 630.54971 -4052.0224 736.3754 14677.94 -19470.208 290.57192 -796.49483 10884.769 1.0034285
10000 23.693652 -3358.3053 637.70114 -3996.0064 727.79701 14741.394 -19469.333 293.86747 -489.17242 10884.769 1.0034285
11000 26.356224 -3382.4087 618.63949 -4001.0482 741.78751 14716.947 -19465.321 285.08342 -330.3192 10884.769 1.0034285
12000 29.112214 -3334.5468 638.43918 -3972.986 747.02393 14738.603 -19465.776 294.20758 -68.170368 10884.769 1.0034285
13000 31.812909 -3371.0486 647.96184 -4019.0104 765.94159 14678.816 -19469.352 298.59584 -97.249564 10884.769 1.0034285
14000 34.538916 -3297.7217 678.51414 -3976.2359 668.98723 14819.716 -19468.779 312.67505 -1268.1136 10884.769 1.0034285
15000 37.266623 -3373.087 639.38201 -4012.469 767.32979 14680.789 -19468.002 294.64205 171.53467 10884.769 1.0034285
16000 40.009645 -3402.4215 652.00299 -4054.4245 771.91001 14636.237 -19469.143 300.45809 -197.81675 10884.769 1.0034285
17000 42.748199 -3354.9429 642.32354 -3997.2664 782.37106 14681.343 -19466.539 295.99758 514.80071 10884.769 1.0034285
18000 45.577128 -3344.8765 654.36132 -3999.2378 753.06347 14710.625 -19468.472 301.54486 26.607457 10884.769 1.0034285
19000 48.37701 -3369.9861 651.23758 -4021.2236 682.11084 14757.597 -19469.739 300.10537 -1381.4838 10884.769 1.0034285
20000 51.238304 -3372.16 644.79106 -4016.9511 761.96533 14683.158 -19468.941 297.13467 33.694074 10884.769 1.0034285
21000 54.015707 -3391.5503 634.23099 -4025.7813 728.48913 14708.684 -19469.76 292.26834 -694.66683 10884.769 1.0034285
22000 56.748778 -3332.257 649.13725 -3981.3943 739.20186 14741.91 -19467.548 299.13749 0.53749352 10884.769 1.0034285
23000 59.447737 -3334.7011 648.36185 -3983.063 763.34358 14713.701 -19466.712 298.78017 351.84157 10884.769 1.0034285
24000 62.111912 -3311.1433 671.52415 -3982.6675 741.0101 14733.039 -19466.072 309.4539 -399.81499 10884.769 1.0034285
25000 64.685375 -3386.7822 632.09186 -4018.8741 740.02281 14704.199 -19470.911 291.28258 -1002.7393 10884.769 1.0034285
26000 67.048266 -3430.0077 621.11236 -4051.12 816.18615 14595.604 -19467.786 286.22297 850.44682 10884.769 1.0034285
27000 69.2054 -3417.9883 652.66224 -4070.6505 746.17234 14644.289 -19468.924 300.76189 -501.95941 10884.769 1.0034285
28000 71.879128 -3352.973 634.50476 -3987.4777 792.88584 14678.588 -19466.619 292.3945 529.47638 10884.769 1.0034285
29000 74.522808 -3418.1756 641.58878 -4059.7643 821.6061 14579.297 -19465.982 295.65899 805.47244 10884.769 1.0034285
30000 77.171838 -3343.4995 663.09171 -4006.5912 753.23767 14701.935 -19467.09 305.56803 157.34857 10884.769 1.0034285
31000 79.798534 -3362.1992 607.29189 -3969.4911 719.52107 14770.077 -19466.154 279.85418 -872.39699 10884.769 1.0034285
32000 82.481369 -3377.2456 642.72578 -4019.9714 777.98481 14664.043 -19467.043 296.18294 70.648441 10884.769 1.0034285
33000 85.125024 -3374.4755 677.62709 -4052.1026 776.50672 14634.382 -19467.03 312.26627 -118.61804 10884.769 1.0034285
34000 87.693977 -3391.7554 630.0941 -4021.8495 793.58227 14647.164 -19468.672 290.36197 336.4751 10884.769 1.0034285
35000 89.550172 -3363.8961 653.24835 -4017.1445 783.07559 14658.706 -19466.708 301.03198 831.25835 10884.769 1.0034285
36000 92.042449 -3378.157 630.28905 -4008.4461 749.13541 14702.888 -19465.523 290.45181 -435.24553 10884.769 1.0034285
37000 94.675515 -3396.8788 636.51966 -4033.3984 786.47438 14640.41 -19466.285 293.32302 180.31598 10884.769 1.0034285
38000 97.317783 -3369.1654 656.56119 -4025.7265 820.3147 14615.021 -19466.701 302.55862 848.43605 10884.769 1.0034285
39000 99.949448 -3377.1989 661.29735 -4038.4963 780.48734 14642.238 -19468.079 304.74115 255.92285 10884.769 1.0034285
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41000 105.28411 -3350.2253 658.81357 -4009.0389 730.42814 14719.114 -19464.283 303.59657 -903.03585 10884.769 1.0034285
42000 107.89321 -3355.1829 634.64919 -3989.8321 717.07127 14753.812 -19467.937 292.46106 -820.68512 10884.769 1.0034285
43000 110.2896 -3373.1254 662.48847 -4035.6139 797.42473 14630.014 -19469.184 305.29005 732.6283 10884.769 1.0034285
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46000 118.28419 -3345.3294 647.45671 -3992.7862 751.60875 14720.847 -19469.691 298.36306 -67.285324 10884.769 1.0034285
47000 120.92672 -3374.6939 650.82643 -4025.5203 803.91747 14632.871 -19469.068 299.9159 885.67175 10884.769 1.0034285
48000 123.54131 -3376.5834 656.4403 -4033.0237 728.45645 14702.693 -19469.04 302.50291 -592.86252 10884.769 1.0034285
49000 126.16474 -3302.6257 677.14869 -3979.7744 763.27829 14719.458 -19466.816 312.04582 579.20607 10884.769 1.0034285
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51000 131.48223 -3403.5465 631.70758 -4035.2541 771.11904 14657.269 -19467.996 291.1055 17.264108 10884.769 1.0034285
52000 134.22028 -3369.879 620.83184 -3990.7108 736.45855 14735.253 -19467.571 286.09371 -79.30133 10884.769 1.0034285
53000 137.03314 -3355.713 667.45254 -4023.1655 750.49151 14687.892 -19464.642 307.5776 -204.76425 10884.769 1.0034285
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63000 163.46632 -3349.249 665.61313 -4014.8621 781.57201 14667.451 -19469.657 306.72996 137.78175 10884.769 1.0034285
64000 166.12552 -3296.4818 688.03213 -3984.5139 740.17128 14737.654 -19468.095 317.06115 320.87241 10884.769 1.0034285
65000 168.67528 -3316.3065 672.07188 -3988.3784 777.23737 14696.693 -19467.354 309.7063 636.33474 10884.769 1.0034285
66000 170.35008 -3381.5748 665.59937 -4047.1742 753.27584 14663.084 -19468.005 306.72362 -611.51143 10884.769 1.0034285
67000 172.36153 -3436.1104 638.38336 -4074.4938 771.9136 14620.585 -19469.51 294.18185 -624.63906 10884.769 1.0034285
68000 174.4599 -3331.1812 667.82988 -3999.011 748.29988 14717.236 -19469.158 307.75149 266.97949 10884.769 1.0034285
69000 177.08185 -3353.5416 659.14109 -4012.6827 768.60823 14682.912 -19467.344 303.74749 386.21889 10884.769 1.0034285
70000 179.6983 -3404.6246 632.16162 -4036.7862 813.50016 14614.534 -19469.311 291.31473 749.62239 10884.769 1.0034285
71000 182.3267 -3384.8668 636.17053 -4021.0373 736.18673 14706.881 -19468.253 293.16213 -621.97708 10884.769 1.0034285
72000 184.97665 -3406.7832 639.97066 -4046.7539 802.95794 14614.5 -19468.425 294.91332 747.74532 10884.769 1.0034285
73000 187.63822 -3350.1839 656.01408 -4006.1979 796.29969 14662.092 -19468.075 302.3065 1094.7749 10884.769 1.0034285
74000 190.31152 -3364.0697 641.24144 -4005.3111 708.3915 14751.579 -19468.594 295.49892 -1060.3998 10884.769 1.0034285
75000 192.94703 -3344.0246 619.05004 -3963.0746 714.57627 14787.263 -19469.194 285.27261 -695.76735 10884.769 1.0034285
76000 195.58904 -3348.1396 658.00002 -4006.1396 724.11817 14733.46 -19465.887 303.22166 -500.54075 10884.769 1.0034285
77000 198.23386 -3302.3014 683.31477 -3985.6162 799.39383 14677.221 -19466.192 314.88728 1169.1764 10884.769 1.0034285
78000 200.91817 -3355.1494 652.84212 -4007.9915 766.02973 14691.262 -19469.202 300.84478 -89.602404 10884.769 1.0034285
79000 203.18307 -3338.1582 663.94322 -4002.1014 731.94742 14730.828 -19469.086 305.96043 -514.05802 10884.769 1.0034285
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81000 208.20428 -3420.5065 649.28955 -4069.7961 825.56991 14569.69 -19469.393 299.20768 900.03551 10884.769 1.0034285
82000 210.96477 -3371.4178 650.22749 -4021.6453 718.597 14725.782 -19469.387 299.6399 -869.42154 10884.769 1.0034285
83000 213.62045 -3413.08 644.35951 -4057.4395 799.05883 14609.683 -19470.186 296.9358 159.67984 10884.769 1.0034285
84000 216.12916 -3387.3358 648.4488 -4035.7846 737.86969 14690.171 -19466.51 298.82024 -448.98917 10884.769 1.0034285
85000 217.78977 -3355.3349 651.60638 -4006.9412 763.37146 14691.793 -19467.511 300.27533 211.15989 10884.769 1.0034285
86000 220.24331 -3392.521 649.59384 -4042.1148 731.63559 14691.855 -19469.003 299.3479 -783.61319 10884.769 1.0034285
87000 222.85728 -3346.3695 649.33458 -3995.7041 742.91425 14725.386 -19469.239 299.22843 -339.24385 10884.769 1.0034285
88000 225.03915 -3352.5714 666.78268 -4019.3541 687.63084 14757.357 -19468.462 307.26892 -1587.4069 10884.769 1.0034285
89000 227.65977 -3404.9342 603.96862 -4008.9029 761.27643 14693.623 -19467.157 278.32274 -9.6654117 10884.769 1.0034285
90000 230.33312 -3388.3658 650.41591 -4038.7817 782.96102 14642.793 -19467.954 299.72673 35.503993 10884.769 1.0034285
91000 232.97093 -3345.3341 682.11092 -4027.445 756.44601 14681.236 -19468.634 314.33252 -299.00279 10884.769 1.0034285
92000 235.61364 -3358.6697 681.92535 -4040.595 757.04448 14669.511 -19469.866 314.24701 -352.88605 10884.769 1.0034285
93000 238.19708 -3398.8534 622.43523 -4021.2886 746.45093 14697.035 -19468.344 286.83258 -293.99367 10884.769 1.0034285
94000 240.91931 -3387.6874 625.71972 -4013.4071 785.29423 14668.442 -19469.791 288.34615 380.29332 10884.769 1.0034285
95000 243.45274 -3338.2567 657.14629 -3995.403 707.60283 14757.373 -19466.122 302.82824 -1259.7291 10884.769 1.0034285
96000 245.12248 -3346.2709 643.8836 -3990.1545 723.21226 14750.182 -19466.67 296.71649 -545.5226 10884.769 1.0034285
97000 246.87645 -3304.122 661.68987 -3965.8119 718.72307 14779.498 -19468.737 304.92203 -185.89581 10884.769 1.0034285
98000 248.95971 -3384.1246 633.68902 -4017.8136 713.00288 14734.686 -19468.944 292.01859 -851.96113 10884.769 1.0034285
99000 251.61686 -3317.834 694.86722 -4012.7012 708.60818 14743.924 -19468.702 320.21093 -1099.8099 10884.769 1.0034285
100000 254.37772 -3372.7172 649.88143 -4022.5987 733.96698 14707.79 -19467.51 299.48043 -597.95684 10884.769 1.0034285
101000 256.34824 -3435.4402 625.03479 -4060.475 789.53059 14615.97 -19470.526 288.03052 225.99984 10884.769 1.0034285
102000 258.79934 -3425.5736 639.52625 -4065.0999 750.05378 14650.15 -19467.654 294.70852 -572.89126 10884.769 1.0034285
103000 260.46195 -3333.926 659.51738 -3993.4434 757.30801 14710.804 -19466.38 303.9209 -358.44401 10884.769 1.0034285
104000 262.54144 -3389.8992 631.351 -4021.2502 752.08137 14694.458 -19470.392 290.94118 -237.00267 10884.769 1.0034285
105000 264.6734 -3415.1147 625.29265 -4040.4073 756.35163 14669.962 -19470.415 288.14935 -281.84399 10884.769 1.0034285
106000 266.35046 -3362.2713 666.64093 -4028.9122 728.0197 14707.008 -19467.447 307.20359 -668.83961 10884.769 1.0034285
107000 268.22001 -3430.7377 655.6673 -4086.405 803.62099 14577.727 -19470.435 302.14669 226.49862 10884.769 1.0034285
108000 269.88995 -3361.2862 631.43629 -3992.7225 738.09167 14735.144 -19468.752 290.98048 -382.52042 10884.769 1.0034285
109000 272.0943 -3391.7549 656.64697 -4048.4019 731.46183 14686.123 -19469.336 302.59815 -637.73354 10884.769 1.0034285
110000 274.69862 -3402.8856 654.59929 -4057.4849 754.83158 14652.555 -19468.706 301.65453 -470.27119 10884.769 1.0034285
111000 277.34594 -3407.6623 637.27419 -4044.9365 743.58123 14675.4 -19466.6 293.67072 -760.83259 10884.769 1.0034285
112000 279.95177 -3373.2725 669.32743 -4042.5999 797.16485 14624.093 -19467.521 308.44159 451.16773 10884.769 1.0034285
113000 282.53937 -3374.0439 635.31101 -4009.3549 767.44434 14689.266 -19469.928 292.76604 388.36057 10884.769 1.0034285
114000 285.15729 -3355.1053 672.59494 -4027.7002 808.32237 14629.692 -19469.661 309.94734 1002.8272 10884.769 1.0034285
115000 287.84578 -3359.004 660.70192 -4019.7059 731.84606 14710.561 -19465.158 304.46676 -457.49989 10884.769 1.0034285
116000 290.46333 -3382.5167 641.72191 -4024.2386 826.16333 14616.715 -19470.01 295.72033 1130.134 10884.769 1.0034285
117000 293.11821 -3376.6964 631.64923 -4008.3456 709.40616 14748.01 -19469.103 291.07861 -850.75899 10884.769 1.0034285
118000 295.72339 -3353.0927 647.77555 -4000.8682 772.26793 14687.698 -19465.814 298.50999 456.68483 10884.769 1.0034285
119000 298.37494 -3338.412 676.05272 -4014.4648 782.58297 14667.708 -19467.257 311.54076 274.30478 10884.769 1.0034285
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121000 303.65442 -3379.5503 679.62301 -4059.1733 830.62237 14575.648 -19468.974 313.18604 1031.6905 10884.769 1.0034285
122000 306.36223 -3408.1155 630.17182 -4038.2873 802.12111 14620.834 -19464.787 290.39779 687.35703 10884.769 1.0034285
123000 308.99604 -3385.1654 673.26825 -4058.4336 771.81722 14635.627 -19468.367 310.25762 -169.60669 10884.769 1.0034285
124000 311.61497 -3355.4717 665.61173 -4021.0834 779.70544 14662.198 -19466.818 306.72931 326.71386 10884.769 1.0034285
125000 314.1964 -3413.2915 577.00287 -3990.2943 756.46551 14717.923 -19468.351 265.8963 87.289663 10884.769 1.0034285
126000 316.84482 -3335.2806 678.38541 -4013.666 794.61202 14656.221 -19467.937 312.61572 1020.6936 10884.769 1.0034285
127000 319.50604 -3283.5149 664.32857 -3947.8434 763.02604 14755.259 -19468.246 306.13801 775.93419 10884.769 1.0034285
128000 322.13682 -3373.8856 639.74564 -4013.6312 742.36506 14707.571 -19467.014 294.80962 -398.08325 10884.769 1.0034285
129000 324.77479 -3316.7354 660.34091 -3977.0763 734.87128 14751.597 -19466.088 304.3004 -108.85228 10884.769 1.0034285
130000 327.41946 -3336.2285 646.68776 -3982.9163 723.25776 14755.649 -19465.563 298.00871 -390.60521 10884.769 1.0034285
131000 330.13089 -3333.7546 649.7099 -3983.4645 719.47086 14757.951 -19464.707 299.40138 -469.73629 10884.769 1.0034285
132000 332.77496 -3383.9317 632.88596 -4016.8177 767.51861 14679.273 -19468.121 291.64852 -32.841441 10884.769 1.0034285
133000 335.41413 -3318.103 661.95903 -3980.062 707.29948 14773.969 -19466.422 305.04607 -921.70961 10884.769 1.0034285
134000 338.08896 -3362.1376 675.41033 -4037.548 827.10475 14600.626 -19468.934 311.24474 1229.6827 10884.769 1.0034285
135000 340.76431 -3381.6526 656.57275 -4038.2253 782.67111 14645.401 -19470.416 302.56395 245.81591 10884.769 1.0034285
136000 343.43365 -3377.86 666.41106 -4044.2711 800.49377 14618.43 -19468.939 307.09767 426.56363 10884.769 1.0034285
137000 346.07992 -3382.3726 641.39997 -4023.7726 747.76814 14693.372 -19469.453 295.57198 -536.73743 10884.769 1.0034285
138000 348.78935 -3345.5697 653.26947 -3998.8391 767.24703 14698.378 -19469.453 301.04172 355.60992 10884.769 1.0034285
139000 351.32267 -3355.2993 612.52971 -3967.8291 675.35188 14819.646 -19467.639 282.26789 -1289.0079 10884.769 1.0034285
140000 353.74664 -3333.8551 660.69982 -3994.5549 809.6887 14656.643 -19466.852 304.46579 1016.7326 10884.769 1.0034285
141000 356.38253 -3381.564 643.86441 -4025.4284 803.64094 14635.815 -19468.831 296.70764 299.12721 10884.769 1.0034285
142000 358.90512 -3377.7551 659.76692 -4037.522 767.88666 14657.399 -19467.536 304.03589 -22.768233 10884.769 1.0034285
143000 361.46651 -3349.7929 680.67436 -4030.4673 746.59464 14684.466 -19464.971 313.67052 82.652939 10884.769 1.0034285
144000 363.32116 -3326.6441 660.58291 -3987.227 818.17919 14657.87 -19467.621 304.41192 1317.9243 10884.769 1.0034285
145000 365.50436 -3365.7544 631.42926 -3997.1837 763.96552 14700.804 -19466.086 290.97724 -105.08989 10884.769 1.0034285
146000 368.16025 -3344.4247 649.68837 -3994.1131 727.85648 14742.086 -19467.483 299.39146 -355.03079 10884.769 1.0034285
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428000 1102.4937 -3304.4879 704.60776 -4009.0956 744.40078 14709.513 -19469.945 324.69959 -419.5764 10884.769 1.0034285
429000 1105.1978 -3367.4955 629.82415 -3997.3197 737.69623 14726.621 -19465.699 290.23757 -608.01844 10884.769 1.0034285
430000 1107.9776 -3359.7485 640.48499 -4000.2335 732.29285 14726.999 -19464.513 295.15033 -346.46851 10884.769 1.0034285
431000 1110.7142 -3347.104 644.73531 -3991.8393 713.68197 14753.969 -19466.15 297.10898 -293.93383 10884.769 1.0034285
432000 1113.3394 -3381.7603 627.72534 -4009.4856 772.22908 14681.906 -19469.528 289.27039 66.938654 10884.769 1.0034285
433000 1116.0902 -3288.8666 678.07131 -3966.9379 726.4096 14767.857 -19467.14 312.47098 -257.87815 10884.769 1.0034285
434000 1118.8714 -3291.5454 674.0904 -3965.6358 702.19642 14795.201 -19467.848 310.63648 -772.05848 10884.769 1.0034285
435000 1121.468 -3391.6417 632.62604 -4024.2677 738.25983 14699.554 -19466.935 291.52875 -384.71448 10884.769 1.0034285
436000 1124.0333 -3344.7129 646.74396 -3991.4568 771.38627 14700.271 -19468.64 298.03461 339.23376 10884.769 1.0034285
437000 1126.5789 -3302.6073 677.89365 -3980.501 759.4459 14722.343 -19467.612 312.38911 28.537371 10884.769 1.0034285
438000 1128.318 -3364.6718 641.55328 -4006.2251 740.91385 14715.521 -19468.002 295.64262 -380.48502 10884.769 1.0034285
439000 1130.0254 -3385.4502 642.70576 -4028.156 766.67713 14668.95 -19469.426 296.17371 24.277727 10884.769 1.0034285
440000 1131.7117 -3315.5933 659.40856 -3975.0018 707.82757 14781.992 -19468.232 303.87075 -533.76874 10884.769 1.0034285
441000 1133.4598 -3321.2249 675.81165 -3997.0366 674.39899 14791.898 -19468.547 311.42968 -1579.1482 10884.769 1.0034285
442000 1135.509 -3378.2788 629.00715 -4007.286 744.84214 14708.265 -19466.909 289.86108 -417.85758 10884.769 1.0034285
443000 1138.0897 -3347.3512 681.06795 -4028.4191 780.45036 14655.702 -19470.636 313.8519 466.29191 10884.769 1.0034285
444000 1140.6965 -3306.0196 667.77881 -3973.7984 768.43443 14720.54 -19467.031 307.72795 998.37763 10884.769 1.0034285
445000 1143.4137 -3359.4115 652.18607 -4011.5975 749.17517 14705.804 -19469.995 300.54246 -462.44282 10884.769 1.0034285
446000 1146.0882 -3400.6866 638.48296 -4039.1696 770.98213 14653.713 -19468.296 294.22775 14.127859 10884.769 1.0034285
447000 1148.7462 -3339.717 658.4156 -3998.1326 781.17553 14684.942 -19469.835 303.41317 546.85191 10884.769 1.0034285
448000 1151.4136 -3367.2848 672.00241 -4039.2872 751.24467 14673.694 -19469.197 309.67429 -174.54916 10884.769 1.0034285
449000 1154.0711 -3328.3729 659.83767 -3988.2105 732.17291 14741.557 -19466.596 304.06849 -494.0091 10884.769 1.0034285
450000 1156.6259 -3337.5255 661.94184 -3999.4673 784.51774 14679.254 -19468.465 305.03814 328.61382 10884.769 1.0034285
451000 1159.2697 -3330.7334 657.66586 -3988.3993 726.25777 14749.782 -19468.054 303.06767 -212.21189 10884.769 1.0034285
452000 1161.8783 -3384.5408 641.33226 -4025.873 809.35379 14628.311 -19467.923 295.54077 1242.1271 10884.769 1.0034285
453000 1163.603 -3323.9463 669.74389 -3993.6902 762.37286 14704.877 -19467.149 308.63351 -41.605907 10884.769 1.0034285
454000 1165.4117 -3388.3708 637.69506 -4026.0659 772.06516 14666.891 -19469.388 293.86467 58.308778 10884.769 1.0034285
455000 1167.9492 -3313.4345 668.98978 -3982.4243 741.69499 14739.311 -19469.65 308.286 10.924678 10884.769 1.0034285
456000 1170.4841 -3319.629 666.20391 -3985.8329 722.74186 14754.216 -19467.292 307.0022 -173.81431 10884.769 1.0034285
457000 1173.1046 -3347.2878 664.42517 -4011.713 796.36488 14654.165 -19466.099 306.18252 438.61125 10884.769 1.0034285
458000 1175.3881 -3325.9018 670.16178 -3996.0636 728.82016 14738.861 -19468.61 308.82609 -685.48207 10884.769 1.0034285
459000 1177.0786 -3381.1491 637.51258 -4018.6617 699.89732 14746.318 -19468.809 293.78058 -1074.0738 10884.769 1.0034285
460000 1178.8567 -3289.6056 677.13175 -3966.7373 724.44644 14771.754 -19467.269 312.03801 -213.65158 10884.769 1.0034285
461000 1180.5847 -3301.641 654.04799 -3955.689 816.06614 14694.221 -19468.178 301.40048 1463.8927 10884.769 1.0034285
462000 1183.2712 -3415.5731 612.23371 -4027.8068 714.47196 14720.075 -19465.776 282.13149 -1203.4166 10884.769 1.0034285
463000 1185.9343 -3353.9724 654.21985 -4008.1923 753.41299 14702.337 -19466.777 301.47968 -38.01484 10884.769 1.0034285
464000 1188.5947 -3367.9482 647.70878 -4015.6569 726.02045 14722.772 -19467.551 298.47922 -746.46033 10884.769 1.0034285
465000 1191.3234 -3375.9438 647.43884 -4023.3827 737.8556 14699.946 -19466.301 298.35483 -762.47592 10884.769 1.0034285
466000 1194.148 -3382.0565 633.88101 -4015.9375 728.14268 14719.033 -19467.501 292.10707 -815.52081 10884.769 1.0034285
467000 1196.9729 -3352.4659 660.95022 -4013.4161 720.84255 14731.47 -19468.821 304.58118 -675.61959 10884.769 1.0034285
468000 1199.7465 -3358.6234 652.51372 -4011.1371 726.76551 14723.721 -19468.476 300.69345 -596.5145 10884.769 1.0034285
469000 1202.4646 -3398.6766 639.12087 -4037.7975 761.92233 14665.696 -19467.917 294.52171 -114.65072 10884.769 1.0034285
470000 1205.1556 -3375.5333 653.08366 -4028.617 747.49005 14687.379 -19467.981 300.95609 -560.00991 10884.769 1.0034285
471000 1207.8286 -3373.3315 648.09883 -4021.4303 738.20986 14702.862 -19467.953 298.65897 -172.19402 10884.769 1.0034285
472000 1210.4971 -3332.1041 673.84369 -4005.9478 724.82747 14734.53 -19468.862 310.52279 -328.77865 10884.769 1.0034285
473000 1213.1828 -3330.0829 681.87274 -4011.9556 768.46848 14683.806 -19468.092 314.22276 123.72622 10884.769 1.0034285
474000 1215.8929 -3346.435 642.00938 -3988.4444 758.61878 14714.661 -19469.159 295.85281 -125.13242 10884.769 1.0034285
475000 1218.5329 -3443.8357 614.83964 -4058.6754 781.61539 14624.416 -19468.477 283.33236 -111.5801 10884.769 1.0034285
476000 1221.178 -3400.7974 638.63917 -4039.4366 784.79512 14641.855 -19469.076 294.29974 517.41905 10884.769 1.0034285
477000 1223.8523 -3320.0342 653.14369 -3973.1779 716.07877 14773.753 -19468.532 300.98376 -458.16557 10884.769 1.0034285
478000 1226.5547 -3399.4442 640.11785 -4039.5621 771.08147 14651.622 -19466.562 294.98115 -197.74698 10884.769 1.0034285
479000 1229.1658 -3326.6496 695.49682 -4022.1464 808.20733 14631.903 -19468.159 320.50106 634.31531 10884.769 1.0034285
480000 1231.8425 -3334.6791 658.32148 -3993.0006 773.22972 14697.373 -19468.715 303.3698 446.26474 10884.769 1.0034285
481000 1234.5644 -3359.0137 662.25789 -4021.2716 794.57799 14646.408 -19467.738 305.18379 886.12083 10884.769 1.0034285
482000 1237.2816 -3364.2843 619.48039 -3983.7646 731.30777 14748.159 -19468.063 285.47092 -620.63473 10884.769 1.0034285
483000 1239.8325 -3322.9451 661.28309 -3984.2282 742.40976 14734.131 -19466.312 304.73458 -222.24701 10884.769 1.0034285
484000 1242.6089 -3375.2908 645.07137 -4020.3622 744.66198 14697.014 -19468.175 297.26384 -136.11832 10884.769 1.0034285
485000 1245.3754 -3378.1938 652.70779 -4030.9016 771.21368 14662.803 -19468.64 300.78288 179.33884 10884.769 1.0034285
486000 1248.1668 -3353.6944 663.96968 -4017.6641 747.96436 14695.385 -19467.156 305.97262 -204.89716 10884.769 1.0034285
487000 1250.9451 -3378.5985 618.19475 -3996.7933 802.27888 14660.268 -19465.25 284.87847 758.55561 10884.769 1.0034285
488000 1253.8242 -3383.4314 628.64496 -4012.0763 695.60474 14755.36 -19468.271 289.69417 -1440.2954 10884.769 1.0034285
489000 1256.7123 -3353.4337 639.18453 -3992.6183 776.60327 14693.087 -19469.167 294.55105 679.63676 10884.769 1.0034285
490000 1259.5889 -3402.9615 644.52942 -4047.4909 791.04054 14624.437 -19466.425 297.0141 261.43904 10884.769 1.0034285
491000 1262.4351 -3365.8526 649.37639 -4015.229 759.05805 14688.834 -19468.725 299.2477 -246.75688 10884.769 1.0034285
492000 1265.3213 -3329.7038 665.28344 -3994.9872 756.07131 14712.004 -19468.819 306.57803 -27.238249 10884.769 1.0034285
493000 1268.1117 -3376.8648 643.42854 -4020.2933 794.79336 14647.846 -19467.803 296.50679 636.6427 10884.769 1.0034285
494000 1270.9762 -3365.5727 627.78783 -3993.3605 785.11016 14682.83 -19467.596 289.29919 657.20701 10884.769 1.0034285
495000 1273.8675 -3360.4436 651.89842 -4012.342 699.51635 14748.52 -19466.495 300.40991 -1445.6517 10884.769 1.0034285
496000 1276.7102 -3364.6024 643.94023 -4008.5427 754.26362 14697.764 -19467.441 296.74259 -122.47872 10884.769 1.0034285
497000 1279.5134 -3295.1345 653.2039 -3948.3384 799.24543 14711.358 -19465.575 301.0115 1418.332 10884.769 1.0034285
498000 1282.3841 -3367.7301 630.59081 -3998.3209 761.83084 14703.35 -19468.711 290.59086 99.969115 10884.769 1.0034285
499000 1285.1837 -3309.0757 652.60901 -3961.6847 760.3183 14738.726 -19467.155 300.73736 352.38315 10884.769 1.0034285
500000 1288.0731 -3360.42 669.85238 -4030.2724 780.88169 14655.258 -19469.761 308.68351 410.74767 10884.769 1.0034285
Loop time of 1288.07 on 12 procs for 500000 steps with 1089 atoms
Performance: 33.538 ns/day, 0.716 hours/ns, 388.177 timesteps/s
92.8% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 586.82 | 650.28 | 723.75 | 172.7 | 50.49
Bond | 0.21603 | 0.47536 | 1.0816 | 38.6 | 0.04
Kspace | 261.99 | 333.22 | 394.35 | 230.9 | 25.87
Neigh | 52.434 | 52.566 | 52.723 | 1.3 | 4.08
Comm | 134.36 | 137.58 | 140.67 | 18.6 | 10.68
Output | 0.088694 | 0.094951 | 0.095607 | 0.6 | 0.01
Modify | 91.711 | 92.795 | 93.695 | 7.3 | 7.20
Other | | 21.06 | | | 1.63
Nlocal: 90.7500 ave 99 max 84 min
Histogram: 2 1 2 0 0 3 2 0 1 1
Nghost: 3801.33 ave 3848 max 3759 min
Histogram: 1 1 2 2 1 0 1 3 0 1
Neighs: 32343.8 ave 35671 max 30135 min
Histogram: 3 1 2 1 0 1 2 0 1 1
Total # of neighbors = 388125
Ave neighs/atom = 356.40496
Ave special neighs/atom = 2.0495868
Neighbor list builds = 20690
Dangerous builds = 0
# write_restart restart.*.lmp
write_data data.*.lmp
System init for write_data ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.26771633
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.025848288
estimated relative force accuracy = 7.7841351e-05
using double precision FFTW3
3d grid and FFT values/proc = 1859 144
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Total wall time: 0:30:56

6514
examples/USER/fep/CH4-CF4/bar01/log.lammps
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5003
examples/USER/fep/CH4-CF4/bar10/bar10.fep Normal file
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5003
examples/USER/fep/CH4-CF4/bar10/bar10.lmp
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69
examples/USER/fep/CH4-CF4/bar10/in.bar10.lmp
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@ -16,74 +16,63 @@ pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10
pair_modify tail yes
kspace_style pppm 1.0e-4
pair_coeff 1 1 none # CF-C CF-C
pair_coeff 1 2 none # CF-C HD-
pair_coeff 1 3 none # CF-C F-D
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # CF-C CF-C
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # CF-C HD-
pair_coeff 1 3 lj/cut/coul/long 0.0591 3.2133 # CF-C F-D
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # CF-C Hw
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # CF-C Ow
pair_coeff 2 2 none # HD- HD-
pair_coeff 2 3 none # HD- F-D
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # HD- HD-
pair_coeff 2 3 lj/cut/coul/long 0.0399 2.7157 # HD- F-D
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 0.0 # HD- Hw
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
pair_coeff 3 3 none # F-D F-D
pair_coeff 3 3 lj/cut/coul/long 0.0530 2.9500 # F-D F-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 1.0 # F-D Hw
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 1.0 # F-D Ow
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable nsteps equal 500000
variable nprint equal ${nsteps}/500
variable ndump equal ${nsteps}/100
# variable nrestart equal ${nsteps}/10
variable temp equal 300.0
variable press equal 1.0
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 2.0
timestep 1.0
velocity all create ${temp} 12345
velocity all create ${TK} 12345
thermo_style multi
thermo ${nprint}
fix SHAKE all shake 0.0001 20 0 b 3 a 4
fix fSHAKE all shake 0.0001 20 ${nprint} b 3 a 4
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 500
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 1000
run 200000
reset_timestep 0
unfix NPT
fix NVT all nvt temp ${TK} ${TK} 100
variable dlambda equal 1.0
variable minusdl equal -1.0
variable dqC equal -0.24*v_dlambda+0.48*(1.0-v_dlambda)
variable dqH equal 0.06*v_dlambda
variable dqF equal -0.12*(1.0-v_dlambda)
variable dlambda equal -1.0
variable minusdl equal 1.0
variable dqC equal (0.48+0.24)*v_dlambda
variable dqH equal -0.06*v_dlambda
variable dqF equal -0.12*v_dlambda
compute cFEP all fep ${temp} &
pair lj/cut/coul/long/soft lambda 2 4*5 v_dlambda &
pair lj/cut/coul/long/soft lambda 3 4*5 v_minusdl &
compute FEP all fep ${TK} &
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
atom charge 1 v_dqC &
atom charge 2 v_dqH &
atom charge 3 v_dqF
fix fFEP all ave/time 1 1 100 c_cFEP[1] c_cFEP[2] file bar10.lmp
fix FEP all ave/time 1 1 100 c_FEP[1] c_FEP[2] file bar10.fep
dump TRAJ all custom 5000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H F H O
# compute cRDF all rdf 100 1 1
# fix fRDF all ave/time 20 100 ${nsteps} c_cRDF file rdf.lammps mode vector
# compute cMSD all msd
# fix fMSD all ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
dump_modify dCONF element C H F H O
# restart ${nrestart} restart.*.lmp
run ${nsteps}
run 500000
# write_restart restart.*.lmp
write_data data.*.lmp

978
examples/USER/fep/CH4-CF4/bar10/log.ber10 Normal file
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@ -0,0 +1,978 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.1.lmp
Reading data file ...
orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
2 by 2 by 3 MPI processor grid
reading atoms ...
1089 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
28 = max angles/atom
reading bonds ...
728 bonds
reading angles ...
388 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
8 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
7 = max # of 1-4 neighbors
8 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail yes
kspace_style pppm 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # CF-C CF-C
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # CF-C HD-
pair_coeff 1 3 lj/cut/coul/long 0.0591 3.2133 # CF-C F-D
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # CF-C Hw
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # CF-C Ow
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # HD- HD-
pair_coeff 2 3 lj/cut/coul/long 0.0399 2.7157 # HD- F-D
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 0.0 # HD- Hw
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
pair_coeff 3 3 lj/cut/coul/long 0.0530 2.9500 # F-D F-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 1.0 # F-D Hw
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 1.0 # F-D Ow
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
velocity all create 300 12345
fix SHAKE all shake 0.0001 20 0 b 3 a 4
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
360 = # of frozen angles
find clusters CPU = 0.001 seconds
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
fix NPT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500
fix NPT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 500
fix NPT all npt temp 300 300 100 iso 1 ${PBAR} 500
fix NPT all npt temp 300 300 100 iso 1 1 500
thermo_style custom step cpu etotal ke pe evdwl ecoul elong temp press vol density
thermo 1000
run 200000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.27021277
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.016919794
estimated relative force accuracy = 5.0953457e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 16.37 | 16.38 | 16.39 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 796.45148 972.9364 -176.48492 -201.60386 19459.424 -19434.493 448.35165 1111.1116 19438.038 0.56189244
1000 2.1178791 -3137.174 617.28966 -3754.4636 775.70717 15120.529 -19651.539 284.46138 234.96113 13590.248 0.8036709
2000 4.2998645 -3276.4234 641.32256 -3917.7459 751.03162 14987.012 -19657.347 295.53631 74.246561 11384.231 0.95940486
3000 7.006056 -3344.7647 655.67451 -4000.4393 722.61082 14934.713 -19658.889 302.15002 -668.98748 11199.256 0.97525111
4000 10.02948 -3329.3372 669.38236 -3998.7196 766.90691 14892.648 -19659.221 308.46691 68.476393 11084.228 0.98537187
5000 12.984913 -3284.8346 666.24224 -3951.0768 733.71768 14973.11 -19659.051 307.01987 -210.71817 11079.93 0.9857541
6000 16.029939 -3332.7706 677.96139 -4010.732 776.73605 14869.568 -19658.321 312.42032 -28.984996 11188.825 0.9761603
7000 19.136439 -3385.9008 636.92323 -4022.824 822.09215 14809.969 -19655.868 293.50899 1315.174 10872.656 1.0045463
8000 22.173472 -3432.7582 652.13946 -4084.8977 792.90184 14784.77 -19663.308 300.52098 171.74504 10831.335 1.0083786
9000 25.209932 -3372.9394 642.79844 -4015.7378 763.7926 14877.365 -19657.892 296.21642 11.438126 11015.783 0.99149436
10000 28.247756 -3360.95 640.53103 -4001.481 743.68857 14914.633 -19660.894 295.17155 -528.65739 11106.753 0.98337356
11000 30.860672 -3374.6046 640.08549 -4014.6901 771.61231 14872.599 -19660.053 294.96623 564.27238 10727.24 1.0181638
12000 33.052395 -3311.3632 660.50157 -3971.8648 731.94432 14956.66 -19661.422 304.37444 313.33466 10696.648 1.0210757
13000 35.970903 -3381.3113 630.21256 -4011.5238 777.09053 14871.001 -19660.806 290.41656 459.90117 10755.303 1.0155071
14000 38.723028 -3387.9258 655.6625 -4043.5883 787.87261 14826.636 -19660.279 302.14448 426.93604 10896.563 1.0023424
15000 40.893905 -3361.1521 639.7612 -4000.9133 758.28261 14898.477 -19660.825 294.81679 521.84404 10657.942 1.0247838
16000 43.856431 -3389.8388 648.73303 -4038.5718 784.89421 14837.725 -19663.587 298.95122 412.49791 10870.751 1.0047224
17000 46.91645 -3285.5184 682.68662 -3968.205 741.24607 14949.552 -19660.579 314.59782 -63.901957 10925.109 0.9997234
18000 49.882524 -3365.6832 637.27623 -4002.9594 791.30655 14863.23 -19659.828 293.67166 538.9356 10937.273 0.99861148
19000 52.815576 -3366.8362 657.17381 -4024.01 694.04208 14939.215 -19658.372 302.84093 -1442.5502 11094.009 0.98450314
20000 55.389913 -3308.9271 649.27421 -3958.2013 775.93001 14922.481 -19659.267 299.20061 421.60633 11169.626 0.97783819
21000 58.448587 -3302.9713 641.44437 -3944.4157 731.65794 14982.087 -19659.037 295.59244 251.20854 10751.099 1.0159042
22000 61.115549 -3346.4921 641.46103 -3987.9531 753.77802 14916.096 -19660.744 295.60011 195.02526 10960 0.99654075
23000 63.986095 -3422.1086 620.26433 -4042.3729 719.41672 14895.98 -19661.32 285.83218 -1036.0805 10978.961 0.99481974
24000 66.868286 -3396.7679 637.73877 -4034.5067 745.48672 14877.62 -19660.48 293.88481 -809.38908 10989.643 0.99385275
25000 69.797902 -3378.7951 650.6991 -4029.4942 729.11489 14897.401 -19659.346 299.85723 -532.89655 10883.067 1.0035854
26000 72.764559 -3351.6229 652.65669 -4004.2796 754.53302 14898.1 -19660.62 300.75933 157.46894 10749.611 1.0160449
27000 75.485748 -3400.3587 650.92745 -4051.2861 711.19845 14895.279 -19659.918 299.96246 -922.0713 10696.232 1.0211154
28000 78.462542 -3356.5518 635.11283 -3991.6647 702.75571 14964.179 -19660.204 292.67471 -973.07424 10904.906 1.0015755
29000 81.366015 -3307.582 666.28725 -3973.8692 731.92317 14949.657 -19660.65 307.04061 -863.1943 11225.601 0.97296234
30000 84.082358 -3368.8316 643.31549 -4012.1471 802.01738 14843.665 -19661.651 296.45469 957.26649 10894.386 1.0025427
31000 87.190999 -3355.936 671.05142 -4026.9874 694.84192 14934.614 -19660.355 309.23605 -1301.8085 10922.006 1.0000074
32000 90.239238 -3345.4858 643.00118 -3988.487 778.89782 14889.278 -19660.588 296.30985 305.63786 11032.199 0.99001903
33000 93.226909 -3419.9279 632.32372 -4052.2516 756.57014 14848.636 -19660.89 291.38943 -76.447605 10879.01 1.0039596
34000 96.33186 -3420.1024 623.14171 -4043.2441 751.20343 14862.222 -19660.979 287.15815 -148.789 10614.673 1.0289613
35000 99.443988 -3353.8647 632.01734 -3985.882 780.36142 14889.507 -19659.01 291.24824 678.64872 10870.554 1.0047406
36000 102.51277 -3370.0618 643.51208 -4013.5739 712.54896 14932.507 -19661.648 296.54529 -411.21947 10611.433 1.0292754
37000 105.59828 -3318.6433 671.86768 -3990.511 760.44583 14905.105 -19658.819 309.6122 196.83869 10834.069 1.0081241
38000 108.65175 -3439.7997 617.00503 -4056.8047 773.64719 14825.726 -19658.711 284.33022 105.3722 10804.5 1.0108832
39000 111.02193 -3386.6339 619.69162 -4006.3255 735.039 14915.866 -19659.301 285.56827 -446.75015 10943.426 0.99805009
40000 112.98373 -3338.6751 635.35829 -3974.0334 751.24796 14932.847 -19661.768 292.78783 -121.74161 10929.734 0.99930036
41000 115.30444 -3392.8122 614.8572 -4007.6694 782.56019 14864.231 -19659.035 283.34045 109.96354 10991.424 0.99369166
42000 118.15943 -3308.2678 662.12443 -3970.3922 758.45574 14929.768 -19660.036 305.12229 713.21311 10815.234 1.0098798
43000 120.79268 -3355.3102 663.85047 -4019.1607 723.0514 14914.088 -19660.209 305.91769 -556.96188 10852.855 1.0063791
44000 123.36549 -3356.5852 635.2663 -3991.8515 754.13718 14908.356 -19659.548 292.74544 30.252306 10880.608 1.0038122
45000 126.20012 -3426.3463 653.50487 -4079.8511 790.29635 14786.089 -19660.139 301.15019 148.55058 10936.139 0.99871511
46000 128.97374 -3358.9948 662.1605 -4021.1553 822.98948 14814.483 -19662.356 305.13891 1349.0304 10891.638 1.0027956
47000 131.6911 -3378.361 640.67429 -4019.0353 730.44178 14904.995 -19657.818 295.23757 -770.15494 10973.41 0.99532297
48000 134.63109 -3363.4208 644.52315 -4007.9439 776.53018 14865.65 -19654.803 297.01121 305.34819 10913.83 1.0007566
49000 137.71877 -3344.4615 657.51347 -4001.975 709.17096 14942.387 -19658.102 302.99745 -919.6298 11243.786 0.97138872
50000 140.7368 -3306.6349 669.53942 -3976.1743 752.62992 14925.712 -19656.494 308.53929 104.49198 11033.542 0.9898985
51000 143.73874 -3392.0071 639.56133 -4031.5684 745.50903 14882.159 -19662.125 294.72469 -265.30701 10700.343 1.020723
52000 146.56798 -3373.4189 669.84157 -4043.2605 725.93743 14888.295 -19661.363 308.67852 -917.92603 10999.903 0.99292576
53000 149.55431 -3377.7021 642.32073 -4020.0228 737.30969 14901.838 -19661.96 295.99628 -263.96717 10818.735 1.009553
54000 152.64117 -3412.5078 617.74315 -4030.2509 745.34154 14882.297 -19660.095 284.67036 -446.20999 10765.806 1.0145164
55000 155.71151 -3352.7615 622.65814 -3975.4196 717.04474 14965.397 -19659.572 286.9353 -179.10108 10813.642 1.0100285
56000 158.7384 -3343.8978 643.21129 -3987.109 730.66799 14938.507 -19661.471 296.40667 -145.08058 10838.232 1.0077369
57000 160.87305 -3295.437 708.4704 -4003.9074 761.2564 14889.628 -19656.979 326.47958 -294.25895 11176.799 0.9772106
58000 163.5422 -3394.2471 655.27691 -4049.524 704.24611 14905.439 -19660.595 301.96679 -917.06631 10740.251 1.0169303
59000 166.34066 -3302.8206 672.33898 -3975.1595 757.72324 14922.73 -19658.448 309.82939 854.45339 10575.151 1.0328067
60000 169.48977 -3341.0939 662.1191 -4003.213 766.3794 14890.225 -19662.226 305.11983 -136.18004 10977.619 0.99494137
61000 172.58247 -3323.4989 656.215 -3979.7139 735.32243 14938.56 -19656.229 302.39909 -285.59711 10946.011 0.99781434
62000 175.67488 -3393.8797 637.22448 -4031.1042 788.64265 14836.228 -19657.771 293.64781 410.69713 10904.798 1.0015855
63000 178.78131 -3368.1252 623.65859 -3991.7838 755.12112 14908.671 -19657.575 287.39634 -167.31766 11063.632 0.98720622
64000 181.95298 -3346.6346 663.67839 -4010.313 749.07041 14895.147 -19657.919 305.83839 -26.482046 10976.734 0.99502152
65000 185.02987 -3308.8676 652.86466 -3961.7322 749.90861 14947.123 -19660.254 300.85517 136.75536 11086.941 0.98513082
66000 188.06708 -3298.4838 654.23713 -3952.7209 736.72641 14965.464 -19659.748 301.48763 -130.65309 10997.362 0.9931552
67000 190.85832 -3333.1479 674.93693 -4008.0849 702.12741 14947.279 -19661.338 311.02659 -1078.8851 11050.457 0.98838329
68000 192.76139 -3278.0242 668.63576 -3946.66 688.83538 15019.323 -19658.79 308.12286 -831.5252 11079.96 0.9857515
69000 195.00463 -3316.8045 648.51037 -3965.3149 701.22978 14992.019 -19661.247 298.84861 -1072.5124 11208.403 0.97445521
70000 197.88957 -3349.0176 670.22471 -4019.2424 750.02725 14886.77 -19658.826 308.85508 -16.730915 10940.653 0.99830305
71000 199.82707 -3371.1933 639.5987 -4010.792 775.22378 14868.66 -19658.897 294.74191 694.31109 10718.745 1.0189707
72000 202.33645 -3355.7001 641.65852 -3997.3586 739.74012 14917.846 -19658.191 295.69112 -268.62285 10755.576 1.0154814
73000 205.17044 -3376.499 633.34827 -4009.8473 728.45963 14919.091 -19660.755 291.86157 -1056.8005 11043.623 0.98899494
74000 207.88122 -3386.081 644.38668 -4030.4677 749.61041 14877.149 -19661.706 296.94832 -191.36624 10937.661 0.99857607
75000 210.72045 -3358.8629 640.51413 -3999.377 789.26274 14864.461 -19658.184 295.16376 505.51476 10826.242 1.008853
76000 213.67789 -3388.8683 654.12881 -4042.9971 804.39569 14804.781 -19657.153 301.43772 1297.3519 10529.123 1.0373216
77000 216.79663 -3357.1653 669.61102 -4026.7764 759.9809 14870.965 -19662.538 308.57228 317.9752 10728.406 1.0180531
78000 219.87387 -3381.1822 630.48763 -4011.6698 733.10358 14913.112 -19659.789 290.54331 -684.10012 10981.061 0.99462945
79000 222.90491 -3326.1204 663.99093 -3990.1113 732.60198 14935.007 -19660.353 305.98241 -135.8725 10981.954 0.9945486
80000 225.96147 -3379.6217 656.04765 -4035.6693 751.71458 14869.506 -19662.118 302.32196 56.565926 10661.81 1.024412
81000 229.10066 -3357.5334 641.77888 -3999.3123 739.88923 14916.649 -19661.458 295.74659 -653.71401 10912.05 1.0009198
82000 232.14074 -3334.4311 657.29638 -3991.7275 747.59119 14918.339 -19661.799 302.89741 251.73339 10870.103 1.0047823
83000 235.23213 -3417.3168 628.27286 -4045.5897 719.93427 14889.812 -19657.317 289.5227 -996.00116 10944.185 0.99798083
84000 238.31303 -3394.3696 649.15959 -4043.5291 763.98012 14847.394 -19657.368 299.14779 -454.13625 11085.054 0.98529844
85000 241.37181 -3324.7667 690.5945 -4015.3612 793.73448 14844.258 -19657.275 318.24195 976.7504 10806.249 1.0107195
86000 244.44614 -3381.9285 663.55685 -4045.4854 796.69708 14815.479 -19659.947 305.78238 1000.4997 10779.733 1.0132057
87000 246.83979 -3378.8578 675.88866 -4054.7465 755.04157 14847.331 -19660.783 311.46516 -516.90953 10896.479 1.0023501
88000 249.12724 -3346.2594 664.68172 -4010.9411 797.70685 14850.756 -19662.047 306.30075 661.14928 10980.764 0.99465633
89000 251.624 -3324.8167 658.82016 -3983.6368 682.94666 14992.076 -19660.096 303.5996 -941.73884 10829.559 1.008544
90000 254.09263 -3323.619 653.91771 -3977.5367 718.47403 14963.289 -19661.073 301.34044 -784.33167 11149.975 0.97956151
91000 257.11595 -3360.1679 635.52364 -3995.6916 762.08329 14896.628 -19658.028 292.86403 -203.5482 11141.502 0.98030647
92000 260.11259 -3333.994 666.22741 -4000.2214 780.85767 14874.475 -19658.425 307.01304 267.99257 11205.853 0.97467696
93000 263.16704 -3330.4971 651.12942 -3981.6265 733.87532 14940.996 -19659.1 300.05553 -526.24523 11044.333 0.98893131
94000 265.31599 -3354.5817 664.39741 -4018.9791 754.99855 14882.393 -19659.307 306.16973 -780.32893 11367.948 0.96077912
95000 267.65193 -3312.1413 655.16877 -3967.3101 716.81709 14972.147 -19659.775 301.91696 -492.99968 10918.007 1.0003736
96000 270.66601 -3334.6146 665.03826 -3999.6528 782.1841 14873.628 -19657.366 306.46505 866.90593 10819.828 1.0094511
97000 273.68623 -3360.8095 640.85175 -4001.6612 762.98405 14892.357 -19659.69 295.31934 170.74108 10794.795 1.0117919
98000 276.72169 -3317.8301 656.1979 -3974.028 784.12965 14901.217 -19661.303 302.3912 502.89547 11074.333 0.98625233
99000 279.75079 -3365.3336 620.04757 -3985.3812 725.83981 14947.068 -19660.647 285.73229 -599.5875 11059.812 0.98754724
100000 282.87128 -3424.2223 625.13175 -4049.354 784.54333 14823.791 -19659.33 288.0752 236.8686 10730.603 1.0178446
101000 285.88363 -3384.9158 635.04518 -4019.961 718.59682 14919.391 -19660.143 292.64354 -585.17723 10704.74 1.0203038
102000 288.81563 -3389.21 642.27452 -4031.4845 756.97025 14870.747 -19661.6 295.97499 -71.057469 10883.364 1.003558
103000 291.91444 -3382.5023 653.83898 -4036.3412 805.70766 14815.581 -19661.431 301.30416 1269.1149 10581.745 1.0321631
104000 295.04233 -3394.9283 648.60109 -4043.5294 753.89542 14861.136 -19661.466 298.89042 304.11019 10611.67 1.0292524
105000 298.08057 -3359.698 662.48213 -4022.1802 728.98523 14905.232 -19660.332 305.28712 -465.30457 10748.747 1.0161266
106000 301.14341 -3354.9197 647.65812 -4002.5778 805.62025 14847.558 -19658.489 298.45588 1173.77 10893.186 1.0026531
107000 304.22724 -3320.6917 684.932 -4005.6237 725.70763 14926.639 -19660.362 315.63254 -482.72539 10946.895 0.99773376
108000 307.35086 -3392.2613 651.11147 -4043.3728 805.84675 14805.912 -19657.462 300.04726 809.6814 10823.66 1.0090936
109000 310.36709 -3344.4238 651.61485 -3996.0386 739.02643 14919.441 -19658.097 300.27923 -436.46078 10972.534 0.99540243
110000 313.41225 -3347.1202 649.42072 -3996.5409 770.11624 14887.39 -19658.593 299.26812 330.9828 10922.97 0.99991918
111000 316.44194 -3353.7911 667.73954 -4021.5306 672.89881 14963.638 -19661.828 307.70986 -1882.6261 11055.042 0.98797331
112000 319.53953 -3350.3916 647.27266 -3997.6642 756.63903 14901.965 -19659.112 298.27825 -238.23736 11055.706 0.98791398
113000 322.62885 -3309.2625 650.72133 -3959.9838 710.21281 14984.97 -19658.662 299.86747 -158.9845 10840.924 1.0074867
114000 325.71347 -3384.6902 630.89701 -4015.5872 762.8435 14879.769 -19659.874 290.73197 111.63981 10913.585 1.000779
115000 328.73526 -3287.8822 694.22546 -3982.1077 716.31133 14956.653 -19657.98 319.91518 -1156.6803 11286.825 0.96768463
116000 331.53563 -3315.983 656.47561 -3972.4586 795.74337 14890.57 -19661.354 302.51918 753.65832 11018.041 0.99129117
117000 334.4488 -3348.667 625.25174 -3973.9187 790.55913 14892.915 -19661.033 288.13049 566.42984 11065.292 0.98705817
118000 337.4592 -3366.9224 635.82586 -4002.7482 755.38856 14899.869 -19662.229 293.00329 -198.51408 10911.276 1.0009907
119000 340.35852 -3305.0654 660.63677 -3965.7021 711.52258 14979.052 -19658.369 304.43674 -86.614123 10743.749 1.0165993
120000 343.23717 -3417.3375 622.00605 -4039.3435 727.77649 14893.102 -19663.165 286.63481 -293.14217 10654.377 1.0251268
121000 346.01542 -3357.918 674.81593 -4032.7339 727.11428 14898.167 -19660.766 310.97082 -633.79575 10835.61 1.0079808
122000 348.93624 -3360.3317 665.07838 -4025.4101 759.26263 14874.623 -19662.174 306.48354 151.45003 10693.31 1.0213944
123000 351.99912 -3412.0181 640.67875 -4052.6968 766.08001 14839.24 -19660.259 295.23962 205.95885 10702.635 1.0205044
124000 355.04022 -3278.8311 635.89219 -3914.7233 671.15345 15070.182 -19658.449 293.03386 -1183.6781 11054.982 0.98797871
125000 358.16591 -3386.4029 640.18891 -4026.5918 784.78353 14843.728 -19659.099 295.01389 325.74695 10893.562 1.0026185
126000 361.15058 -3433.9016 622.38584 -4056.2875 727.37366 14876.347 -19663.451 286.80982 -1038.9896 10946.28 0.99778985
127000 364.11465 -3349.3076 655.0774 -4004.385 763.37375 14883.51 -19656.035 301.87485 -218.4718 11085.104 0.98529401
128000 367.05631 -3339.0931 626.19766 -3965.2907 720.96067 14969.801 -19659.646 288.5664 -859.58403 11164.212 0.97831242
129000 369.82577 -3346.5322 680.51576 -4027.048 771.13094 14859.986 -19661.265 313.59744 324.004 10891.283 1.0028283
130000 372.57168 -3439.7255 635.6154 -4075.3409 805.01634 14776.315 -19661.649 292.90631 -115.49488 10939.054 0.99844891
131000 375.32325 -3307.7761 691.75317 -3999.5293 755.30916 14905.425 -19663.215 318.7759 81.880397 10887.391 1.0031868
132000 378.09982 -3388.2977 654.22524 -4042.5229 747.15553 14867.45 -19660.76 301.48216 190.52151 10651.19 1.0254334
133000 380.94449 -3384.94 654.35668 -4039.2967 748.8742 14870.882 -19661.092 301.54273 -541.01657 10844.487 1.0071557
134000 383.7839 -3407.6402 624.84343 -4032.4836 774.97903 14849.539 -19661.683 287.94234 133.81081 10844.896 1.0071177
135000 386.61704 -3359.6634 670.10754 -4029.771 756.31413 14870.242 -19659.474 308.80109 63.113655 10821.315 1.0093123
136000 389.46211 -3382.261 630.92636 -4013.1873 734.67421 14905.21 -19659.114 290.74549 -1083.8007 11063.719 0.98719851
137000 392.24723 -3365.9813 634.50886 -4000.4901 741.17998 14915.079 -19659.506 292.39639 -187.81356 10923.406 0.99987926
138000 395.03504 -3353.7085 646.75511 -4000.4636 815.12165 14837.948 -19657.096 298.03975 1649.4459 10668.284 1.0237904
139000 397.89795 -3380.2196 634.4666 -4014.6862 742.16735 14900.35 -19660.374 292.37692 -319.39752 10786.89 1.0125335
140000 400.66819 -3330.5989 657.0196 -3987.6185 752.66316 14914.623 -19659.716 302.76986 -318.68873 11131.675 0.98117194
141000 403.54006 -3367.4498 603.19547 -3970.6452 824.1362 14862.08 -19660.738 277.96646 1438.5379 11070.588 0.98658599
142000 406.35918 -3330.7577 668.74521 -3999.5029 664.85502 14989.466 -19657.795 308.1733 -1862.2996 11088.891 0.98495754
143000 409.19765 -3381.7701 608.32915 -3990.0993 723.50214 14945.969 -19662.92 280.33218 -633.19689 10906.717 1.0014092
144000 412.07612 -3410.3169 628.35826 -4038.6751 757.63746 14855.963 -19657.484 289.56205 -187.13502 10826.37 1.0088411
145000 414.91289 -3365.3473 647.06629 -4012.4136 742.0013 14903.442 -19661.697 298.18315 -421.16208 10987.066 0.99408582
146000 417.77049 -3376.8539 654.17852 -4031.0324 715.49185 14910.393 -19661.789 301.46063 -852.17172 10701.136 1.0206474
147000 420.69489 -3257.5396 700.88336 -3958.423 732.69568 14967.053 -19661.415 322.9833 307.93031 10890.859 1.0028674
148000 423.5606 -3370.6566 640.17598 -4010.8326 741.48808 14901.667 -19659.35 295.00793 -431.04255 10981.29 0.99460872
149000 426.41536 -3417.4353 636.74525 -4054.1806 762.29561 14838.793 -19659.835 293.42697 170.63908 10545.441 1.0357165
150000 429.22737 -3374.4532 645.7685 -4020.2217 740.60439 14897.529 -19661.726 297.58509 -284.00874 10834.9 1.0080469
151000 432.06296 -3342.683 650.39477 -3993.0778 741.32188 14921.249 -19659.531 299.71699 265.34275 10596.239 1.0307513
152000 434.70681 -3339.9678 666.9058 -4006.8736 781.55709 14865.062 -19658.412 307.32565 304.09161 10927.201 0.999532
153000 437.64467 -3392.5258 654.42152 -4046.9474 755.1475 14853.388 -19658.578 301.57261 -139.79905 10815.536 1.0098517
154000 440.59104 -3379.9628 643.77563 -4023.7385 810.93581 14822.067 -19661.222 296.66673 951.32837 10934.923 0.99882612
155000 443.79125 -3387.157 653.5319 -4040.6889 719.87271 14896.957 -19660.533 301.16265 -1187.5171 11026.766 0.99050682
156000 446.90223 -3337.9608 646.62242 -3984.5832 745.0894 14927.653 -19659.671 297.9786 -157.20261 10938.792 0.99847283
157000 450.17421 -3355.7815 643.98662 -3999.7681 814.39316 14841.752 -19660.628 296.76397 1175.8758 10966.876 0.99591594
158000 453.38203 -3278.6076 662.68104 -3941.2886 771.39393 14943.059 -19659.158 305.37879 646.7184 10928.917 0.99937501
159000 456.53875 -3322.9035 673.4448 -3996.3483 816.50684 14843.74 -19660.696 310.33897 1420.1814 10690.96 1.0216189
160000 459.14736 -3359.5945 662.50336 -4022.0979 753.49747 14881.129 -19662.166 305.2969 403.42443 10654.995 1.0250673
161000 462.02353 -3340.2143 660.52013 -4000.7344 833.29527 14821.175 -19658.452 304.38299 1690.2541 10765.107 1.0145823
162000 464.78063 -3315.1616 638.18042 -3953.342 733.51367 14969.511 -19659.934 294.08833 -11.410296 10762.789 1.0148008
163000 467.72185 -3414.8517 660.56527 -4075.417 784.94697 14796.249 -19660.745 304.40379 717.17786 10607.408 1.0296659
164000 470.86361 -3392.5227 635.49213 -4028.0149 744.10606 14885.663 -19659.894 292.84951 -484.79847 10822.346 1.0092161
165000 473.97945 -3370.5939 635.64081 -4006.2347 735.69635 14914.837 -19659.221 292.91802 -366.20675 10732.848 1.0176318
166000 477.00901 -3351.9259 662.73663 -4014.6625 754.47609 14887.005 -19659.53 305.4044 347.92099 10812.13 1.0101698
167000 479.92829 -3324.8585 682.5223 -4007.3808 741.55118 14906.258 -19658.32 314.5221 -312.59063 10986.888 0.994102
168000 483.03934 -3385.9671 608.49721 -3994.4643 799.73792 14864.419 -19661.057 280.40962 996.09172 10734.734 1.017453
169000 486.10721 -3363.1368 666.31755 -4029.4543 798.24615 14831.781 -19662.556 307.05458 1171.7075 10751.753 1.0158424
170000 489.16761 -3340.8253 654.42857 -3995.2538 695.60616 14966.164 -19660.825 301.57586 -1081.5065 10991.874 0.99365107
171000 492.18751 -3369.9132 647.91166 -4017.8249 779.49077 14860.846 -19663.261 298.57271 439.1861 10681.767 1.0224981
172000 495.23199 -3279.0991 675.98169 -3955.0807 808.81599 14890.264 -19657.617 311.50804 2078.4207 10692.897 1.0214338
173000 498.22219 -3346.3465 634.06962 -3980.4161 706.77967 14969.535 -19661.012 292.19398 -500.64414 10818.755 1.0095511
174000 501.25773 -3319.4978 675.05736 -3994.5551 752.95312 14909.169 -19659.612 311.08208 -164.78094 11020.702 0.99105181
175000 504.24479 -3419.6514 623.99952 -4043.6509 719.50252 14892.82 -19659.434 287.55345 -1023.3189 10899.184 1.0021013
176000 507.26801 -3365.6575 658.97556 -4024.6331 779.26542 14853.65 -19661.063 303.67121 452.22531 10739.576 1.0169943
177000 510.34611 -3376.2528 638.11848 -4014.3713 731.62896 14909.638 -19659.342 294.05979 -880.97848 10990.902 0.99373891
178000 513.42892 -3400.8487 673.42455 -4074.2732 832.06208 14749.718 -19659.167 310.32964 1337.4358 10743.509 1.0166219
179000 516.52946 -3316.1651 661.15445 -3977.3195 781.57106 14898.739 -19661.801 304.6753 989.22559 10953.456 0.99713614
180000 519.66411 -3363.0125 622.13259 -3985.145 735.01185 14936.549 -19660.757 286.69312 -724.92051 10938.257 0.99852171
181000 522.76771 -3419.7374 649.38245 -4069.1199 728.39068 14859.398 -19659.343 299.25049 -1000.9797 10906.425 1.001436
182000 526.01134 -3370.1782 639.49004 -4009.6683 740.02839 14907.731 -19660.171 294.69183 -233.58514 10872.834 1.0045299
183000 529.25129 -3390.4796 626.61079 -4017.0904 826.51423 14812.674 -19659.793 288.75678 1627.8211 10689.408 1.0217672
184000 532.54084 -3415.5959 649.88609 -4065.482 793.66482 14798.685 -19661.081 299.48258 417.93747 10885.821 1.0033315
185000 535.72795 -3397.5662 630.39485 -4027.961 768.92995 14859.523 -19659.862 290.50056 383.4633 10701.224 1.020639
186000 538.93875 -3418.3605 649.84969 -4068.2102 783.92147 14804.565 -19659.175 299.4658 72.04256 10797.031 1.0115824
187000 542.08291 -3432.4487 585.95407 -4018.4028 786.2218 14852.57 -19659.276 270.02122 336.11138 10899.119 1.0021074
188000 545.20217 -3373.1116 672.17332 -4045.2849 772.99626 14839.215 -19661.12 309.75305 -58.493651 11043.151 0.98903714
189000 548.2169 -3295.273 668.9156 -3964.1886 703.61731 14987.479 -19657.926 308.25182 -799.25148 11047.547 0.98864366
190000 551.30564 -3414.4996 625.65276 -4040.1524 783.95452 14836.123 -19662.015 288.3153 427.29632 10746.51 1.016338
191000 554.26501 -3347.84 630.45947 -3978.2995 734.98451 14943.479 -19659.113 290.53034 -484.20843 11065.698 0.98702195
192000 557.33857 -3377.5308 624.6704 -4002.2012 777.34284 14876.908 -19658.478 287.8626 393.02771 11017.223 0.99136481
193000 560.33376 -3337.0899 656.75025 -3993.8402 771.40143 14890.2 -19658.528 302.64574 284.94044 10931.971 0.99909588
194000 563.37771 -3373.4236 635.77963 -4009.2032 742.75456 14903.858 -19658.671 292.98199 -591.29578 11133.219 0.98103585
195000 566.21382 -3338.2396 634.71832 -3972.9579 718.30184 14965.507 -19659.862 292.49292 -971.9023 11224.966 0.97301737
196000 569.19125 -3384.8433 613.31046 -3998.1538 792.41129 14866.921 -19660.368 282.62768 849.20195 10804.94 1.010842
197000 572.16142 -3364.543 656.04681 -4020.5898 728.40423 14911.697 -19662.873 302.32158 -558.1508 10885.879 1.0033262
198000 575.14492 -3280.6737 667.84991 -3948.5237 721.09287 14984.947 -19657.751 307.76072 -372.17558 10831.286 1.0083832
199000 578.24469 -3353.5271 646.52939 -4000.0565 763.56646 14890.737 -19658.516 297.93573 90.341544 10870.612 1.0047352
200000 581.16527 -3429.7279 650.20138 -4079.9293 778.52437 14798.897 -19661.287 299.62787 450.35651 10639.538 1.0265565
Loop time of 581.165 on 12 procs for 200000 steps with 1089 atoms
Performance: 29.733 ns/day, 0.807 hours/ns, 344.136 timesteps/s
93.1% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 228.82 | 259.13 | 298.53 | 122.0 | 44.59
Bond | 0.14595 | 0.29354 | 0.74599 | 37.7 | 0.05
Kspace | 117.63 | 157.71 | 187.59 | 156.3 | 27.14
Neigh | 21.524 | 21.568 | 21.609 | 0.6 | 3.71
Comm | 54.506 | 59.432 | 62.273 | 37.7 | 10.23
Output | 0.012463 | 0.012863 | 0.016908 | 1.1 | 0.00
Modify | 61.03 | 67.602 | 80.939 | 93.1 | 11.63
Other | | 15.41 | | | 2.65
Nlocal: 90.7500 ave 99 max 85 min
Histogram: 3 0 2 1 1 1 2 1 0 1
Nghost: 3840.92 ave 3901 max 3811 min
Histogram: 5 0 1 1 1 1 1 1 0 1
Neighs: 33120.1 ave 37893 max 30075 min
Histogram: 2 1 1 3 2 1 1 0 0 1
Total # of neighbors = 397441
Ave neighs/atom = 364.95960
Ave special neighs/atom = 2.0495868
Neighbor list builds = 8482
Dangerous builds = 4
reset_timestep 0
unfix NPT
fix NVT all nvt temp ${TK} ${TK} 100
fix NVT all nvt temp 300 ${TK} 100
fix NVT all nvt temp 300 300 100
variable dlambda equal -1.0
variable minusdl equal 1.0
variable dqC equal (0.48+0.24)*v_dlambda
variable dqH equal -0.06*v_dlambda
variable dqF equal -0.12*v_dlambda
compute FEP all fep ${TK} pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda atom charge 1 v_dqC atom charge 2 v_dqH atom charge 3 v_dqF
compute FEP all fep 300 pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda atom charge 1 v_dqC atom charge 2 v_dqH atom charge 3 v_dqF
fix FEP all ave/time 1 1 100 c_FEP[1] c_FEP[2] file bar10.fep
dump TRAJ all custom 5000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H F H O
run 500000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.26835398
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.025279937
estimated relative force accuracy = 7.6129779e-05
using double precision FFTW3
3d grid and FFT values/proc = 1859 144
FEP settings ...
temperature = 300.000000
tail no
lj/cut/coul/long/soft lambda 2-2 4-5
lj/cut/coul/long/soft lambda 3-3 4-5
1-1 charge
2-2 charge
3-3 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 17.62 | 17.63 | 17.63 Mbytes
Step CPU TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Volume Density
0 0 -3429.7922 650.20138 -4079.9936 778.52437 14663.799 -19526.253 299.62787 652.44739 10639.538 1.0265565
1000 2.7291422 -3450.6489 627.65424 -4078.3032 773.09784 14672.144 -19527.38 289.23762 59.67731 10639.538 1.0265565
2000 5.1716057 -3411.1345 620.56028 -4031.6948 809.89478 14683.189 -19527.769 285.96856 1462.7183 10639.538 1.0265565
3000 7.968929 -3427.5817 620.61297 -4048.1947 743.70039 14728.628 -19524.873 285.99284 -169.8359 10639.538 1.0265565
4000 10.834602 -3403.2917 623.25508 -4026.5468 767.68486 14725.525 -19524.184 287.21039 326.00696 10639.538 1.0265565
5000 13.693019 -3398.6065 636.38865 -4034.9951 759.72668 14726.811 -19524.365 293.26264 339.02075 10639.538 1.0265565
6000 16.533551 -3350.3057 652.78337 -4003.0891 764.35861 14751.967 -19524.454 300.81771 924.9462 10639.538 1.0265565
7000 19.253912 -3404.2832 670.21174 -4074.495 797.68565 14650.122 -19526.546 308.84911 533.3195 10639.538 1.0265565
8000 21.98252 -3371.3579 633.26103 -4004.6189 765.53416 14754.118 -19528.868 291.82136 700.42144 10639.538 1.0265565
9000 24.761323 -3363.913 657.76407 -4021.6771 762.55784 14736.432 -19524.862 303.11293 758.26965 10639.538 1.0265565
10000 27.510869 -3401.5672 649.32487 -4050.8921 803.02799 14667.781 -19525.977 299.22395 843.31476 10639.538 1.0265565
11000 30.308727 -3347.4148 659.3343 -4006.7491 728.76885 14786.68 -19525.337 303.83653 -348.62865 10639.538 1.0265565
12000 33.046295 -3411.9309 631.62777 -4043.5587 739.27973 14736.625 -19522.624 291.06872 -112.04497 10639.538 1.0265565
13000 35.575513 -3336.6583 650.41649 -3987.0748 752.70474 14780.905 -19523.349 299.727 322.72663 10639.538 1.0265565
14000 38.318888 -3382.7861 622.52704 -4005.3132 723.07035 14794.511 -19526.565 286.87489 -435.11698 10639.538 1.0265565
15000 40.923487 -3333.6311 690.50768 -4024.1388 809.79607 14686.722 -19524.038 318.20195 1315.9762 10639.538 1.0265565
16000 43.687979 -3408.64 629.9852 -4038.6252 735.79701 14746.634 -19526.286 290.31179 -254.91498 10639.538 1.0265565
17000 46.348893 -3423.3863 664.92129 -4088.3076 774.67755 14660.484 -19527.251 306.41115 13.155463 10639.538 1.0265565
18000 48.82842 -3361.6345 668.13913 -4029.7736 798.59159 14693.375 -19525.65 307.894 1259.4192 10639.538 1.0265565
19000 51.655868 -3349.2045 640.57789 -3989.7824 682.0504 14846.425 -19521.726 295.19314 -839.68398 10639.538 1.0265565
20000 54.624731 -3381.8901 674.30239 -4056.1925 812.96864 14651.917 -19524.988 310.73417 967.53452 10639.538 1.0265565
21000 57.445658 -3450.3503 637.03485 -4087.3851 833.76363 14601.791 -19525.692 293.56043 1307.6822 10639.538 1.0265565
22000 59.982307 -3420.9198 641.54018 -4062.46 809.12541 14650.544 -19525.127 295.63659 1282.2755 10639.538 1.0265565
23000 61.650047 -3399.1907 670.79208 -4069.9828 734.87706 14716.918 -19526.181 309.11654 -812.01885 10639.538 1.0265565
24000 63.693927 -3350.4532 674.17602 -4024.6292 776.94118 14721.839 -19526.089 310.67594 795.85597 10639.538 1.0265565
25000 66.474644 -3376.3911 677.04069 -4053.4318 783.65072 14684.348 -19526.032 311.99604 654.00846 10639.538 1.0265565
26000 69.167773 -3412.2885 642.43253 -4054.721 788.91637 14677.434 -19524.422 296.0478 307.72803 10639.538 1.0265565
27000 71.722682 -3439.8653 640.77286 -4080.6382 735.34045 14708.075 -19527.761 295.28299 -513.82263 10639.538 1.0265565
28000 74.336554 -3336.374 674.97319 -4011.3472 761.61859 14748.269 -19524.199 311.04329 358.85449 10639.538 1.0265565
29000 77.031292 -3348.963 681.51639 -4030.4794 758.98334 14734.901 -19526.745 314.05855 46.410876 10639.538 1.0265565
30000 79.797171 -3411.5693 632.42108 -4043.9904 796.2695 14679.101 -19524.341 291.43429 1045.1191 10639.538 1.0265565
31000 82.483715 -3338.7018 663.69187 -4002.3937 752.18681 14765.022 -19523.547 305.8446 511.97171 10639.538 1.0265565
32000 84.683009 -3391.1486 645.45562 -4036.6042 778.0448 14706.763 -19525.265 297.44091 416.85358 10639.538 1.0265565
33000 86.566625 -3369.3021 635.54203 -4004.8442 785.69823 14728.037 -19523.904 292.8725 939.00644 10639.538 1.0265565
34000 88.797298 -3362.4966 640.34124 -4002.8378 819.7279 14698.796 -19523.896 295.08409 1551.4306 10639.538 1.0265565
35000 90.944058 -3350.7449 650.94087 -4001.6858 761.8998 14753.821 -19521.664 299.96865 336.21971 10639.538 1.0265565
36000 93.403027 -3335.3558 655.18314 -3990.5389 737.12427 14789.809 -19521.292 301.92358 504.32156 10639.538 1.0265565
37000 96.06302 -3356.0052 636.3317 -3992.3369 722.11298 14809.397 -19526.614 293.2364 -208.83514 10639.538 1.0265565
38000 98.743705 -3420.9057 599.90014 -4020.8058 821.11624 14679.801 -19524.467 276.44789 1400.327 10639.538 1.0265565
39000 101.47237 -3411.5611 677.26273 -4088.8238 812.42695 14618.619 -19523.876 312.09837 1335.4487 10639.538 1.0265565
40000 104.15155 -3385.2785 636.06559 -4021.3441 757.66174 14745.495 -19527.066 293.11377 522.68756 10639.538 1.0265565
41000 106.94707 -3358.7323 668.21543 -4026.9477 737.54344 14758.158 -19526.717 307.92916 -120.17777 10639.538 1.0265565
42000 109.74407 -3420.2257 638.85491 -4059.0806 732.64594 14731.151 -19526.771 294.39915 -416.21524 10639.538 1.0265565
43000 112.18704 -3355.0504 646.10454 -4001.1549 783.61076 14734.907 -19523.912 297.73995 997.96062 10639.538 1.0265565
44000 114.86356 -3369.773 656.54091 -4026.3139 792.89064 14701.324 -19525.171 302.54927 1178.815 10639.538 1.0265565
45000 117.65448 -3345.3679 653.62598 -3998.9938 700.58855 14817.227 -19522.587 301.206 -406.11634 10639.538 1.0265565
46000 120.49276 -3342.2174 654.71008 -3996.9275 825.5742 14697.909 -19524.204 301.70558 1789.6769 10639.538 1.0265565
47000 123.41476 -3344.5757 664.75177 -4009.3275 758.71862 14747.98 -19522.362 306.33303 293.32658 10639.538 1.0265565
48000 126.32958 -3355.7535 637.16455 -3992.918 743.03625 14787.882 -19528.96 293.6202 358.19484 10639.538 1.0265565
49000 129.03755 -3355.9515 672.84468 -4028.7962 767.40704 14724.747 -19523.491 310.06243 755.5964 10639.538 1.0265565
50000 131.97426 -3404.0342 645.96341 -4049.9976 787.92262 14681.847 -19525.293 297.67491 778.66192 10639.538 1.0265565
51000 134.04972 -3410.1015 652.43717 -4062.5387 809.4301 14647.951 -19524.104 300.65817 903.03684 10639.538 1.0265565
52000 136.77299 -3379.743 637.0683 -4016.8113 803.33313 14700.477 -19526.191 293.57584 1277.2462 10639.538 1.0265565
53000 139.51815 -3349.8944 640.79766 -3990.6921 763.57782 14762.409 -19525.009 295.29442 503.04198 10639.538 1.0265565
54000 142.2336 -3358.8485 641.68935 -4000.5379 794.92237 14726.13 -19525.883 295.70533 1205.7962 10639.538 1.0265565
55000 144.90981 -3401.3416 661.07081 -4062.4125 785.43388 14674.535 -19526.181 304.63676 750.70851 10639.538 1.0265565
56000 147.27339 -3330.9118 632.2723 -3963.1841 780.11058 14775.696 -19525.607 291.36573 1511.3127 10639.538 1.0265565
57000 149.22047 -3355.9074 630.47665 -3986.384 770.90443 14766.605 -19526.533 290.53826 991.90206 10639.538 1.0265565
58000 151.92614 -3340.0679 682.71741 -4022.7853 795.37774 14702.475 -19524.989 314.61201 937.85942 10639.538 1.0265565
59000 154.66636 -3422.4041 637.02033 -4059.4245 778.60352 14681.802 -19523.521 293.55373 94.354954 10639.538 1.0265565
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131000 343.5876 -3369.8782 663.75533 -4033.6335 797.37699 14685.934 -19526.374 305.87384 1260.4077 10639.538 1.0265565
132000 346.33827 -3395.6051 643.3618 -4038.9669 786.50545 14691.586 -19525.396 296.47603 475.67507 10639.538 1.0265565
133000 349.10464 -3375.4495 619.71621 -3995.1657 737.71422 14780.832 -19523.677 285.5796 214.74059 10639.538 1.0265565
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344000 884.15591 -3391.1809 642.71024 -4033.8911 845.36038 14636.696 -19527.265 296.17578 2151.7862 10639.538 1.0265565
345000 886.91847 -3396.902 623.02471 -4019.9267 826.15534 14672.196 -19525.478 287.10423 1417.5488 10639.538 1.0265565
346000 889.67873 -3369.6368 617.98532 -3987.6221 756.54855 14773.913 -19523.563 284.78196 712.81989 10639.538 1.0265565
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349000 897.86005 -3399.7581 658.53312 -4058.2912 814.02384 14648.496 -19527.634 303.46733 1045.0751 10639.538 1.0265565
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465000 1204.6369 -3459.6779 655.97645 -4115.6543 829.97465 14574.093 -19527.892 302.28916 1246.7583 10639.538 1.0265565
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467000 1209.8388 -3445.4704 635.89649 -4081.3669 804.6257 14629.626 -19523.747 293.03585 553.20582 10639.538 1.0265565
468000 1212.513 -3386.6045 638.37975 -4024.9843 780.26052 14710.784 -19523.025 294.18019 653.79582 10639.538 1.0265565
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470000 1217.8497 -3388.2603 635.45218 -4023.7124 832.08568 14665.575 -19526.939 292.8311 1554.0435 10639.538 1.0265565
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473000 1224.4471 -3359.5351 675.67061 -4035.2057 800.36206 14681.389 -19523.562 311.36468 945.32236 10639.538 1.0265565
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475000 1229.4616 -3367.8183 662.99939 -4030.8177 742.62425 14743.98 -19526.294 305.52549 -320.36761 10639.538 1.0265565
476000 1232.1373 -3387.9887 666.85094 -4054.8397 793.08948 14671.181 -19525.541 307.30037 655.94078 10639.538 1.0265565
477000 1234.7676 -3408.8083 620.23963 -4029.048 824.6931 14664.873 -19524.607 285.8208 1208.4684 10639.538 1.0265565
478000 1237.1581 -3354.4346 668.20442 -4022.639 778.3753 14716.366 -19525.168 307.92409 384.21846 10639.538 1.0265565
479000 1239.6541 -3413.8106 681.22039 -4095.031 782.48199 14643.469 -19527.271 313.92215 135.62132 10639.538 1.0265565
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481000 1244.6926 -3362.9927 674.11278 -4037.1055 781.0387 14698.44 -19526.099 310.6468 326.87373 10639.538 1.0265565
482000 1246.3403 -3386.8508 648.3913 -4035.2421 817.27659 14664.278 -19527.279 298.79374 1023.4811 10639.538 1.0265565
483000 1248.5022 -3329.1708 643.19844 -3972.3692 784.5872 14757.566 -19524.288 296.40075 1268.6505 10639.538 1.0265565
484000 1251.1315 -3380.0256 643.96409 -4023.9897 799.46607 14695.035 -19525.635 296.75358 1189.3236 10639.538 1.0265565
485000 1253.8401 -3405.867 644.74752 -4050.6146 858.28163 14604.973 -19521.369 297.1146 2159.9916 10639.538 1.0265565
486000 1256.5506 -3411.3815 648.87548 -4060.257 815.66913 14640.973 -19523.844 299.01686 1415.2985 10639.538 1.0265565
487000 1259.2426 -3405.9256 602.94129 -4008.8669 712.81579 14796.051 -19525.911 277.84932 -628.12772 10639.538 1.0265565
488000 1261.9614 -3454.2703 627.31799 -4081.5883 726.92846 14707.297 -19523.227 289.08267 -1022.6864 10639.538 1.0265565
489000 1264.6655 -3413.5062 615.05924 -4028.5655 760.39823 14732.349 -19525.707 283.43356 260.75689 10639.538 1.0265565
490000 1267.3524 -3401.4934 674.81226 -4076.3056 822.85108 14624.026 -19528.161 310.96913 1152.2172 10639.538 1.0265565
491000 1270.0283 -3361.4052 661.93732 -4023.3425 734.7952 14759.743 -19528.032 305.03606 -151.55868 10639.538 1.0265565
492000 1272.7907 -3349.6241 654.51842 -4004.1425 734.51915 14780.697 -19526.7 301.61726 6.3946976 10639.538 1.0265565
493000 1275.5215 -3330.5851 658.39164 -3988.9767 752.1748 14779.398 -19526.163 303.40213 496.47386 10639.538 1.0265565
494000 1278.2445 -3336.5102 649.77232 -3986.2825 782.34351 14752.257 -19527.335 299.43015 1034.0107 10639.538 1.0265565
495000 1280.418 -3328.6491 638.26242 -3966.9115 740.6229 14812.192 -19524.072 294.12612 304.87682 10639.538 1.0265565
496000 1282.1825 -3363.1016 649.1262 -4012.2278 752.71881 14752.009 -19525.494 299.1324 312.7941 10639.538 1.0265565
497000 1284.8717 -3402.8304 627.45153 -4030.2819 788.4971 14703.325 -19526.303 289.14421 1021.3167 10639.538 1.0265565
498000 1287.623 -3365.7262 650.65787 -4016.384 796.89937 14706.694 -19525.663 299.83823 1175.4544 10639.538 1.0265565
499000 1290.3914 -3404.2959 632.16529 -4036.4612 807.86409 14677.334 -19526.407 291.31642 976.25608 10639.538 1.0265565
500000 1293.1313 -3323.2228 670.09598 -3993.3188 828.12519 14697.624 -19523.988 308.79576 1972.7006 10639.538 1.0265565
Loop time of 1293.13 on 12 procs for 500000 steps with 1089 atoms
Performance: 33.407 ns/day, 0.718 hours/ns, 386.658 timesteps/s
92.9% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 591.52 | 655.55 | 743.52 | 160.8 | 50.69
Bond | 0.18405 | 0.47277 | 1.2806 | 48.9 | 0.04
Kspace | 247.66 | 334.37 | 395.83 | 219.3 | 25.86
Neigh | 51.914 | 52.013 | 52.143 | 1.0 | 4.02
Comm | 135.24 | 137.48 | 140.12 | 13.7 | 10.63
Output | 0.08753 | 0.093122 | 0.093741 | 0.6 | 0.01
Modify | 90.987 | 92.158 | 93.08 | 7.3 | 7.13
Other | | 20.99 | | | 1.62
Nlocal: 90.7500 ave 99 max 85 min
Histogram: 4 1 0 1 0 2 2 1 0 1
Nghost: 3831.50 ave 3885 max 3787 min
Histogram: 1 3 0 1 2 2 0 1 1 1
Neighs: 33067.3 ave 36833 max 28064 min
Histogram: 1 0 1 1 2 1 2 2 0 2
Total # of neighbors = 396808
Ave neighs/atom = 364.37833
Ave special neighs/atom = 2.0495868
Neighbor list builds = 20585
Dangerous builds = 0
# write_restart restart.*.lmp
write_data data.*.lmp
System init for write_data ...
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.26835398
grid = 12 12 12
stencil order = 5
estimated absolute RMS force accuracy = 0.025279937
estimated relative force accuracy = 7.6129779e-05
using double precision FFTW3
3d grid and FFT values/proc = 1859 144
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/coul/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Total wall time: 0:31:14

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22
examples/USER/fep/CH4-CF4/fep01/fep01.fep Normal file
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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.00312019 10865.2 10850.6
200000 0.010508 10744 10861.8
300000 0.0264291 10420.9 10812
400000 0.0545079 9994.3 10846.2
500000 0.088714 9488.72 10855.7
600000 0.153339 8601.91 10821.5
700000 0.182336 8320.98 10867
800000 0.212811 8058.45 10837
900000 0.251228 7661.29 10862.6
1000000 0.213228 8157.05 10859.6
1100000 0.183075 8503.26 10863.4
1200000 0.135028 9031.32 10833.1
1300000 0.108265 9395.91 10834.6
1400000 0.0515654 10271.1 10891.2
1500000 0.032442 10524.7 10838.1
1600000 -0.0020387 11085.9 10839.4
1700000 -0.0471478 11927.5 10867.5
1800000 -0.0642882 12270.2 10875
1900000 -0.0996282 12928.6 10844.2
2000000 -0.123813 13495.3 10894.9

94
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@ -0,0 +1,94 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.0.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail yes
kspace_style pppm 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C-CF C-CF
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C-CF H-D
pair_coeff 1 3 lj/cut/coul/long 0.0591 3.2133 # C-CF FD-
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # C-CF Hw
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # C-CF Ow
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H-D H-D
pair_coeff 2 3 lj/cut/coul/long 0.0399 2.7157 # H-D FD-
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 1.0 # H-D Hw
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 1.0 # H-D Ow
pair_coeff 3 3 lj/cut/coul/long 0.0530 2.9500 # FD- FD-
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 0.0 # FD- Hw
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 0.0 # FD- Ow
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
fix SHAKE all shake 0.0001 20 0 b 3 a 4
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 1000
run 200000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
variable minusl equal 1.0-v_lambda
variable qC equal 0.48*v_lambda-0.24*(1.0-v_lambda)
variable qH equal 0.06*(1.0-v_lambda)
variable qF equal -0.12*v_lambda
fix ADAPT all adapt/fep 100000 &
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4*5 v_lambda &
atom charge 1 v_qC &
atom charge 2 v_qH &
atom charge 3 v_qF &
after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density &
v_lambda v_qC v_qH v_qF
variable dlambda equal 0.05
variable minusdl equal -0.05
variable dqC equal (0.48+0.24)*v_dlambda
variable dqH equal -0.06*v_dlambda
variable dqF equal -0.12*v_dlambda
compute FEP all fep ${TK} &
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
atom charge 1 v_dqC &
atom charge 2 v_dqH &
atom charge 3 v_dqF &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H F H O
run 2000000
# write_restart restart.*.lmp
write_data data.*.lmp

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22
examples/USER/fep/CH4-CF4/fep10/fep10.fep Normal file
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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.137272 8712.14 10903.6
200000 0.108321 9166.67 10895.3
300000 0.0832528 9556.53 10855.2
400000 0.0544891 10066.4 10849.5
500000 0.0344004 10432.6 10865.3
600000 -0.0063993 11270.3 10881.3
700000 -0.0633232 12495.9 10875.6
800000 -0.0498311 12203.1 10878.1
900000 -0.0855723 13133.8 10887.5
1000000 -0.118751 13959.2 10844.1
1100000 -0.134037 14376.7 10860.6
1200000 -0.145443 14494.5 10848.6
1300000 -0.134143 14189 10855.4
1400000 -0.129561 13923.9 10830.6
1500000 -0.132449 13883.2 10851.7
1600000 -0.0731106 12459.2 10832.6
1700000 -0.0310166 11575.4 10881.4
1800000 -0.0130746 11185.2 10855.8
1900000 -0.00967349 11135.5 10875.3
2000000 -0.000553533 10919.7 10840.9

94
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@ -0,0 +1,94 @@
# created by fftool
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.1.lmp
# read_restart restart.*.lmp
# reset_timestep 0
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/coul/long/soft 1 0.5 10.0 10.0 10.0
pair_modify tail yes
kspace_style pppm 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # CF-C CF-C
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # CF-C HD-
pair_coeff 1 3 lj/cut/coul/long 0.0591 3.2133 # CF-C F-D
pair_coeff 1 4 lj/cut/coul/long 0.0000 1.8708 # CF-C Hw
pair_coeff 1 5 lj/cut/coul/long 0.1013 3.3286 # CF-C Ow
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # HD- HD-
pair_coeff 2 3 lj/cut/coul/long 0.0399 2.7157 # HD- F-D
pair_coeff 2 4 lj/cut/coul/long/soft 0.0000 1.5811 0.0 # HD- Hw
pair_coeff 2 5 lj/cut/coul/long/soft 0.0683 2.8131 0.0 # HD- Ow
pair_coeff 3 3 lj/cut/coul/long 0.0530 2.9500 # F-D F-D
pair_coeff 3 4 lj/cut/coul/long/soft 0.0000 1.7176 1.0 # F-D Hw
pair_coeff 3 5 lj/cut/coul/long/soft 0.0908 3.0559 1.0 # F-D Ow
pair_coeff 4 4 lj/cut/coul/long 0.0000 1.0000 # Hw Hw
pair_coeff 4 5 lj/cut/coul/long 0.0000 1.7792 # Hw Ow
pair_coeff 5 5 lj/cut/coul/long 0.1554 3.1655 # Ow Ow
variable TK equal 300.0
variable PBAR equal 1.0
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
fix SHAKE all shake 0.0001 20 0 b 3 a 4
fix NPT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 1000
run 200000
reset_timestep 0
variable lambda equal ramp(1.0,0.0)
variable minusl equal 1.0-v_lambda
variable qC equal 0.48*v_lambda-0.24*(1.0-v_lambda)
variable qH equal 0.06*(1.0-v_lambda)
variable qF equal -0.12*v_lambda
fix ADAPT all adapt/fep 100000 &
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusl &
pair lj/cut/coul/long/soft lambda 3 4*5 v_lambda &
atom charge 1 v_qC &
atom charge 2 v_qH &
atom charge 3 v_qF &
after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density &
v_lambda v_qC v_qH v_qF
variable dlambda equal -0.05
variable minusdl equal 0.05
variable dqC equal (0.48+0.24)*v_dlambda
variable dqH equal -0.06*v_dlambda
variable dqF equal -0.12*v_dlambda
compute FEP all fep ${TK} &
pair lj/cut/coul/long/soft lambda 2 4*5 v_minusdl &
pair lj/cut/coul/long/soft lambda 3 4*5 v_dlambda &
atom charge 1 v_dqC &
atom charge 2 v_dqH &
atom charge 3 v_dqF &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H F H O
run 2000000
# write_restart restart.*.lmp
write_data data.*.lmp

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39
examples/USER/fep/CH4hyd/README → examples/USER/fep/CH4hyd/README.md
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@ -2,13 +2,14 @@ Free Energy of Hydration of Methane
===================================
Example calculation of the free energy of hydration of methane with
LAMMPS using *compute fep* and *fix adapt/fep*.
LAMMPS using *compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.
Methane is represented by the 5-site OPLS-AA model (1 molecule). Water
is represented by the 4-site TIP4P-Ew model (360 molecules). Interactions
of sites that are being created or deleted are treated using soft-core
verions of the Lennard-Jones and Coulomb potentials (*pair
lj/cut/coul/long/soft*) in order to avoid singularities.
of sites that are being created or deleted are treated using Lennard-Jones
and Coulomb potentials with soft cores (*pair lj/cut/coul/long/soft*)
in order to avoid singularities. Trajectories are at constant NpT, so
corrections for the fluctuating volume are included.
The following directories contain input files and results for
calculations using free-energy perturbation (FEP) and
@ -19,39 +20,37 @@ finite-difference thermodynamic integration (FDTI):
`data.lmp`
* `fep01` -- Calculation using FEP, multi-stage creation of a methane
molecule. Results in `fep01.lmp`
molecule. Results in `fep01.fep`
* `fep10` -- Calculation using FEP, multi-stage deletion of a methane
molecule. Results in `fep10.lmp`
molecule. Results in `fep10.fep`
* `fdti01` -- Calculation using TI/FDTI, creation of a methane
molecule. Results in `fdti01.lmp`
molecule. Results in `fdti01.fep`
* `fdti10` -- Calculation using TI/FDTI, deletion a methane
molecule. Results in `fdti10.lmp`
molecule. Results in `fdti10.fep`
The free-energy profiles can be observed by plotting the values in the
third column of the results files. The Python scripts `fep.py`,
`nti.py` and `fdti.py` found in the `tools` directory can be used to
calculate the free-energy differences corresponding to the above
transformations:
The Python scripts `fep.py`, `fdti.py` and `fti.py` found in the
`tools` directory can be used to calculate the free-energy differences
corresponding to the transformations above:
fep.py 300 < fep01.lmp
fep.py 300 < fep01.fep
fep.py 300 < fep10.lmp
fep.py 300 < fep10.fep
nti.py 300 0.002 < fdti01.lmp
fdti.py 300 0.002 < fdti01.fep
nti.py 300 0.002 < fdti10.lmp
fdti.py 300 0.002 < fdti10.fep
fdti.py 300 0.002 < fdti01.lmp
nti.py 300 0.002 < fdti01.fep
fdti.py 300 0.002 < fdti10.lmp
nti.py 300 0.002 < fdti10.fep
The outputs are in kcal/mol and can be compared with the experimental
value of 2.0 kcal/mol, or with a simulation value from the literature
obtained with the same force field models used here: 2.27 kcal/mol
[MR Shirts, VS Pande, J Chem Phys 122 (2005) 134508].
[MR Shirts, VS Pande, J Chem Phys 122 (2005) 134508](https://doi.org/10.1063/1.1877132).
These example calculations are for tutorial purposes only. The results
may not be of research quality (not enough sampling, size of the step

23
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@ -0,0 +1,23 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.000825924 10909.6 10924.6
200000 0.0058514 10827 10933.6
300000 0.0126833 10711.5 10941
400000 0.0220624 10570.7 10967.3
500000 0.0232183 10542 10954.7
600000 0.0200945 10633.6 10991.8
700000 0.0135137 10734.9 10974.7
800000 0.0106469 10775.9 10966.1
900000 0.00498044 10888.1 10977.1
1000000 0.00197392 10981.8 11016.4
1100000 0.00179706 10935.5 10967.1
1200000 -0.000595793 11007.2 10995.5
1300000 -0.0011627 11018.8 10996.7
1400000 -0.00136585 11021.1 10995.1
1500000 -0.00227648 11027.6 10985.2
1600000 -0.00317171 11058.8 10999.8
1700000 -0.003654 11094 11026.1
1800000 -0.00445653 11077.2 10994.5
1900000 -0.00533782 11097.2 10998.2
2000000 -0.00623909 11080.4 10965
2100000 -0.00663295 11076.8 10954.2

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

25
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp
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@ -41,7 +41,7 @@ timestep 1.0
velocity all create ${TK} 12345
thermo_style multi
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
@ -49,6 +49,7 @@ fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
set type 1*2 charge 0.0
run 100000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
@ -61,7 +62,7 @@ fix ADAPT all adapt/fep 100000 &
atom charge 2 v_q2 &
after yes
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal 0.002
variable dq1 equal -0.24*v_dlambda
@ -70,14 +71,28 @@ variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} &
pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2
atom charge 2 v_dq2 &
volume yes
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[*] file fdti01.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000
unfix ADAPT
# perturb at lambda = 1 to 1.002
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

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@ -0,0 +1,803 @@
LAMMPS (29 Oct 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# created by fftool
print "Methane in TIP4P water"
Methane in TIP4P water
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.lmp
Reading data file ...
orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
2 by 2 by 3 MPI processor grid
reading atoms ...
1085 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
724 bonds
reading angles ...
366 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.013 seconds
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm/tip4p 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 0.0 # C4H Ow
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # C4H Hw
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
variable TK equal 300.0
variable PBAR equal 1.0
fix SHAKE all shake 0.0001 20 0 b 2 a 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
360 = # of frozen angles
find clusters CPU = 0.001 seconds
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
velocity all create 300 12345
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 1 1000
set type 1*2 charge 0.0
Setting atom values ...
5 settings made for charge
run 100000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.27021504
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.025869595
estimated relative force accuracy = 7.7905518e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.87 | 10.88 | 10.90 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density
0 548.49163 647.43194 -98.940309 -203.16773 29916.943 -29812.884 300 792.60653 0.55642578
5000 -3289.6503 661.8139 -3951.4642 745.98638 25311.37 -30009.296 306.66415 59.150479 0.99224242
10000 -3264.0347 685.09114 -3949.1258 773.73595 25289.123 -30012.539 317.45011 777.39342 0.98636787
15000 -3251.5551 648.11398 -3899.6691 671.398 25441.786 -30013.334 300.31603 -413.14206 1.016661
20000 -3252.4 689.36359 -3941.7636 737.7343 25333.597 -30013.526 319.42983 -21.174789 0.97535351
25000 -3338.3947 615.37903 -3953.7737 787.76879 25271.858 -30013.71 285.14767 1017.286 0.99756551
30000 -3284.3985 677.49887 -3961.8974 762.04248 25284.899 -30009.413 313.93209 244.39314 0.97967112
35000 -3261.5411 666.45457 -3927.9957 733.96743 25351.027 -30013.599 308.8145 -110.12637 0.96937976
40000 -3234.8532 623.53317 -3858.3863 713.89789 25437.451 -30010.345 288.92605 8.4228945 0.97303537
45000 -3355.6584 635.78023 -3991.4386 847.07484 25173.275 -30012.205 294.60096 1998.0377 1.0016853
50000 -3289.0168 631.74466 -3920.7614 746.01676 25347.251 -30014.586 292.731 72.499979 0.98411892
55000 -3317.0357 623.56712 -3940.6028 761.336 25307.662 -30010.219 288.94178 631.58596 0.99041384
60000 -3235.6514 670.35907 -3906.0105 763.2789 25342.581 -30012.557 310.62372 485.74187 0.96692138
65000 -3289.6272 631.91655 -3921.5438 726.6807 25361.327 -30009.98 292.81065 -39.822331 0.98670912
70000 -3356.7387 634.65207 -3991.3908 759.18886 25260.804 -30011.846 294.0782 -279.67723 0.96104105
75000 -3339.1035 646.63311 -3985.7366 740.57966 25283.92 -30010.741 299.62985 -663.63274 0.97015795
80000 -3315.2349 629.58698 -3944.8219 703.81392 25361.66 -30010.869 291.7312 -274.07447 1.0083118
85000 -3287.7679 646.81739 -3934.5853 715.97889 25360.677 -30011.833 299.71524 -446.21411 0.99175345
90000 -3328.6167 643.38471 -3972.0014 799.56485 25239.915 -30011.926 298.12464 1554.6031 1.0204346
95000 -3309.6011 644.25764 -3953.8587 772.13317 25285.772 -30012.282 298.52913 714.97326 0.99859772
100000 -3234.6909 663.02311 -3897.714 742.089 25372.74 -30012.966 307.22446 626.49142 0.98804377
Loop time of 690.837 on 12 procs for 100000 steps with 1085 atoms
Performance: 12.507 ns/day, 1.919 hours/ns, 144.752 timesteps/s
96.8% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 428.72 | 462.98 | 490.39 | 77.4 | 67.02
Bond | 0.082724 | 0.1141 | 0.1569 | 6.2 | 0.02
Kspace | 113.99 | 141.18 | 174.95 | 138.6 | 20.44
Neigh | 10.442 | 10.477 | 10.513 | 0.6 | 1.52
Comm | 28.443 | 31.702 | 33.282 | 30.0 | 4.59
Output | 0.0012247 | 0.0012662 | 0.0016445 | 0.3 | 0.00
Modify | 31.689 | 35.472 | 43.676 | 76.6 | 5.13
Other | | 8.913 | | | 1.29
Nlocal: 90.4167 ave 99 max 79 min
Histogram: 1 1 0 0 2 2 1 1 3 1
Nghost: 3895.83 ave 3960 max 3844 min
Histogram: 2 3 0 1 0 1 1 2 1 1
Neighs: 0.833333 ave 6 max 0 min
Histogram: 10 0 0 0 0 0 1 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 4076
Dangerous builds = 1
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix ADAPT all adapt/fep 100000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda atom charge 1 v_q1 atom charge 2 v_q2 after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal 0.002
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
compute FEP all fep 300 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fdti01.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28574247
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014533761
estimated relative force accuracy = 4.3767988e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
FEP settings ...
temperature = 300.000000
tail no
lj/cut/tip4p/long/soft lambda 1-2 3-4
1-1 charge
2-2 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.17 | 12.18 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_q1 v_q2
0 -3234.7709 663.02311 -3897.794 742.089 27095.239 -31735.545 307.22446 699.17165 0.98804377 0 -0 0
5000 -3289.0224 631.33682 -3920.3592 731.99995 27081.876 -31734.814 292.54202 -179.44137 0.99284002 0.0025 -0.0006 0.00015
10000 -3299.1847 676.16148 -3975.3462 708.59345 27050.107 -31734.496 313.31238 -518.83651 0.99067088 0.005 -0.0012 0.0003
15000 -3302.2326 642.06473 -3944.2973 725.78424 27062.847 -31733.405 297.513 -508.19421 0.98063265 0.0075 -0.0018 0.00045
20000 -3296.4091 644.34799 -3940.7571 742.59645 27053.208 -31737.038 298.57099 116.68509 0.99271503 0.01 -0.0024 0.0006
25000 -3329.7456 639.23547 -3968.9811 783.76339 26982.097 -31735.383 296.20201 496.16152 0.97684075 0.0125 -0.003 0.00075
30000 -3290.8879 622.28019 -3913.1681 761.24177 27062.793 -31737.656 288.34545 1324.9373 1.020133 0.015 -0.0036 0.0009
35000 -3258.8976 654.70358 -3913.6012 720.26437 27101.834 -31736.017 303.36945 -12.98411 0.98568197 0.0175 -0.0042 0.00105
40000 -3316.6813 661.50653 -3978.1879 744.40073 27012.054 -31735.136 306.52173 -328.49176 0.98122496 0.02 -0.0048 0.0012
45000 -3328.8398 626.57382 -3955.4137 767.73554 27012.692 -31736.292 290.33499 216.96405 0.98739876 0.0225 -0.0054 0.00135
50000 -3340.9891 657.35839 -3998.3475 830.88061 26901.969 -31731.639 304.59961 1277.8313 0.9894139 0.025 -0.006 0.0015
55000 -3286.6334 664.03418 -3950.6675 693.37215 27091.208 -31735.635 307.69297 -1169.7207 0.97446921 0.0275 -0.0066 0.00165
60000 -3284.1129 649.62828 -3933.7411 742.27197 27058.071 -31734.367 301.01772 217.61495 0.99138135 0.03 -0.0072 0.0018
65000 -3278.0768 656.07593 -3934.1527 802.64294 26995.676 -31733.004 304.00536 1438.6113 0.99167193 0.0325 -0.0078 0.00195
70000 -3257.071 646.97756 -3904.0486 784.2684 27041.692 -31730.549 299.78945 1105.7892 0.97904694 0.035 -0.0084 0.0021
75000 -3302.3867 616.53809 -3918.9247 724.15443 27092.319 -31735.774 285.68474 -257.61941 0.98545045 0.0375 -0.009 0.00225
80000 -3273.1943 666.82395 -3940.0182 710.93871 27084.085 -31735.513 308.98566 -793.05223 0.97840301 0.04 -0.0096 0.0024
85000 -3265.5621 673.58344 -3939.1455 718.18264 27076.343 -31734.09 312.1178 -266.75978 0.99570803 0.0425 -0.0102 0.00255
90000 -3290.206 653.64139 -3943.8474 639.00442 27149.273 -31732.703 302.87727 -2090.0779 0.98198222 0.045 -0.0108 0.0027
95000 -3331.8751 640.75522 -3972.6303 741.43112 27017.822 -31732.42 296.90621 -273.00408 0.98683047 0.0475 -0.0114 0.00285
100000 -3296.8724 646.00751 -3942.8799 692.35792 27098.667 -31734.399 299.33996 -1122.9346 0.96037747 0.05 -0.012 0.003
105000 -3323.043 660.68623 -3983.7293 725.81149 27024.038 -31733.834 306.14163 -478.30302 1.0026308 0.0525 -0.0126 0.00315
110000 -3293.647 644.60735 -3938.2544 773.7496 27021.39 -31733.875 298.69117 434.89378 0.96738408 0.055 -0.0132 0.0033
115000 -3318.6094 617.95787 -3936.5672 711.01122 27087.703 -31735.935 286.34262 -586.06437 0.9963844 0.0575 -0.0138 0.00345
120000 -3318.7136 619.55912 -3938.2728 711.36644 27085.947 -31736.008 287.08459 -174.13483 1.0014176 0.06 -0.0144 0.0036
125000 -3311.5169 619.86219 -3931.3791 740.06281 27062.525 -31734.232 287.22503 95.093205 0.98984372 0.0625 -0.015 0.00375
130000 -3257.5389 660.71935 -3918.2582 743.22185 27073.512 -31735.593 306.15698 691.41882 1.0024 0.065 -0.0156 0.0039
135000 -3234.1888 663.45494 -3897.6437 703.73158 27132.827 -31734.715 307.42456 -485.33417 0.96446007 0.0675 -0.0162 0.00405
140000 -3328.5262 611.78779 -3940.314 758.21124 27032.974 -31731.986 283.4836 291.77762 0.99457944 0.07 -0.0168 0.0042
145000 -3324.8731 622.90615 -3947.7792 753.6117 27033.123 -31735.186 288.6355 343.24728 1.0157261 0.0725 -0.0174 0.00435
150000 -3326.137 623.51882 -3949.6559 781.40757 27001.12 -31732.581 288.9194 379.64232 0.97830823 0.075 -0.018 0.0045
155000 -3267.7496 642.82809 -3910.5777 711.45054 27113.985 -31736.481 297.86672 -292.80529 0.99361431 0.0775 -0.0186 0.00465
160000 -3299.5989 662.74649 -3962.3454 712.8089 27056.164 -31731.87 307.09629 -496.04777 0.99183864 0.08 -0.0192 0.0048
165000 -3329.291 646.32489 -3975.6159 801.98506 26958.482 -31736.573 299.48702 997.42028 0.98284724 0.0825 -0.0198 0.00495
170000 -3318.536 653.82172 -3972.3577 786.6347 26975.18 -31734.52 302.96083 1334.3627 1.0236211 0.085 -0.0204 0.0051
175000 -3325.4627 619.69669 -3945.1594 690.02714 27098.09 -31733.687 287.14834 -919.83628 0.99453856 0.0875 -0.021 0.00525
180000 -3300.3031 636.65018 -3936.9533 745.64489 27054.483 -31737.57 295.00406 219.06021 0.99348984 0.09 -0.0216 0.0054
185000 -3203.2521 676.13783 -3879.3899 745.60713 27109.132 -31734.768 313.30143 414.18855 0.9633435 0.0925 -0.0222 0.00555
190000 -3277.3235 646.22256 -3923.546 751.99067 27057.559 -31733.602 299.43961 413.00249 0.98434955 0.095 -0.0228 0.0057
195000 -3346.2223 647.85098 -3994.0733 767.89014 26969.502 -31731.781 300.19417 -28.507593 0.96832487 0.0975 -0.0234 0.00585
200000 -3300.1935 646.69629 -3946.8898 701.64088 27083.477 -31732.446 299.65912 -707.03161 0.99055336 0.1 -0.024 0.006
205000 -3290.9787 648.02246 -3939.0011 640.17442 27153.624 -31733.433 300.27363 -1956.9384 0.98696639 0.1025 -0.0246 0.00615
210000 -3274.8996 636.56925 -3911.4689 749.14043 27072.195 -31733.439 294.96656 57.011756 0.97283184 0.105 -0.0252 0.0063
215000 -3258.8914 649.62228 -3908.5137 730.52403 27095.576 -31734.9 301.01494 332.42518 1.0045487 0.1075 -0.0258 0.00645
220000 -3281.2031 642.14025 -3923.3434 643.85812 27165.046 -31732.913 297.54799 -1558.401 0.99750231 0.11 -0.0264 0.0066
225000 -3242.8112 669.68595 -3912.4972 740.44086 27078.221 -31731.576 310.31182 392.39792 0.98549974 0.1125 -0.027 0.00675
230000 -3352.6039 612.90242 -3965.5063 808.89628 26961.627 -31736.506 284.00008 1238.5363 0.99442962 0.115 -0.0276 0.0069
235000 -3212.4042 663.39662 -3875.8008 756.43457 27102.946 -31735.628 307.39754 758.23141 0.97498485 0.1175 -0.0282 0.00705
240000 -3257.9461 661.57114 -3919.5172 705.4144 27107.544 -31733.064 306.55167 -204.87272 0.99976854 0.12 -0.0288 0.0072
245000 -3316.5321 647.24561 -3963.7777 786.91081 26980.581 -31731.697 299.91366 1202.2468 1.0222577 0.1225 -0.0294 0.00735
250000 -3341.8246 611.9646 -3953.7892 714.94089 27068.038 -31737.283 283.56553 -911.34644 0.96448073 0.125 -0.03 0.0075
255000 -3254.0891 633.16816 -3887.2572 726.85516 27120.339 -31734.945 293.3906 283.04242 0.98991259 0.1275 -0.0306 0.00765
260000 -3299.1746 651.3513 -3950.5259 696.47895 27089.924 -31737.328 301.81611 -871.73224 1.002751 0.13 -0.0312 0.0078
265000 -3293.1078 657.79434 -3950.9021 755.40667 27026.683 -31733.429 304.80161 360.25773 0.9780128 0.1325 -0.0318 0.00795
270000 -3299.6191 650.52447 -3950.1436 755.41579 27026.359 -31732.393 301.43298 435.04681 1.0014121 0.135 -0.0324 0.0081
275000 -3359.4622 653.89684 -4013.3591 765.0782 26956.42 -31735.291 302.99564 225.63288 1.0067016 0.1375 -0.033 0.00825
280000 -3350.239 629.1103 -3979.3493 747.4181 27008.767 -31736.054 291.51031 50.082819 0.99033851 0.14 -0.0336 0.0084
285000 -3296.0733 631.87144 -3927.9447 767.84143 27039.142 -31735.433 292.78974 440.12726 0.98245521 0.1425 -0.0342 0.00855
290000 -3315.5154 631.97291 -3947.4883 735.6925 27051.956 -31735.594 292.83676 -401.59925 0.97468222 0.145 -0.0348 0.0087
295000 -3329.4745 619.27086 -3948.7453 757.72687 27030.731 -31737.727 286.95102 411.84621 0.99363064 0.1475 -0.0354 0.00885
300000 -3271.6999 644.55528 -3916.2552 770.83041 27046.839 -31734.414 298.66704 841.55452 0.98127197 0.15 -0.036 0.009
305000 -3294.5361 647.43638 -3941.9725 776.74162 27015.144 -31734.455 300.00205 961.02872 0.99335699 0.1525 -0.0366 0.00915
310000 -3313.5724 627.74532 -3941.3178 744.36807 27045.425 -31731.541 290.87782 -41.809135 0.97419513 0.155 -0.0372 0.0093
315000 -3291.8842 660.90248 -3952.7867 749.45524 27033.348 -31736.039 306.24183 125.83355 0.97548669 0.1575 -0.0378 0.00945
320000 -3342.0632 640.02001 -3982.0832 748.47758 27004.346 -31735.393 296.56554 -409.30162 0.98147613 0.16 -0.0384 0.0096
325000 -3263.3328 653.53527 -3916.8681 741.0287 27074.791 -31733.038 302.82809 135.82717 0.98928298 0.1625 -0.039 0.00975
330000 -3298.307 649.21354 -3947.5205 734.02868 27052.27 -31734.229 300.82554 -241.90534 0.99122064 0.165 -0.0396 0.0099
335000 -3311.2598 640.76877 -3952.0286 751.60727 27031.457 -31735.578 296.91249 -431.52514 0.96057138 0.1675 -0.0402 0.01005
340000 -3252.2266 682.23754 -3934.4641 750.29336 27049.403 -31734.459 316.12784 291.37614 0.97683555 0.17 -0.0408 0.0102
345000 -3299.3283 655.32395 -3954.6523 766.1933 27010.242 -31731.463 303.65691 454.23332 0.98480505 0.1725 -0.0414 0.01035
350000 -3298.5888 645.51264 -3944.1014 725.64663 27063.717 -31733.902 299.11065 -306.54333 0.98824029 0.175 -0.042 0.0105
355000 -3328.0776 599.92527 -3928.0029 686.38793 27118.323 -31733.001 277.98687 -465.98865 1.0206672 0.1775 -0.0426 0.01065
360000 -3286.4378 665.88662 -3952.3244 718.96631 27061.135 -31732.89 308.55133 -996.9909 0.95139192 0.18 -0.0432 0.0108
365000 -3339.4175 603.25117 -3942.6687 683.48081 27110.189 -31736.738 279.52799 -1038.6806 0.98977996 0.1825 -0.0438 0.01095
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1665000 -3252.9457 694.14474 -3947.0905 712.30879 27076.129 -31737.086 321.64527 -646.87417 0.96762975 0.8325 -0.1998 0.04995
1670000 -3305.871 619.27179 -3925.1428 737.61963 27073.074 -31737.532 286.95145 60.456806 0.98147319 0.835 -0.2004 0.0501
1675000 -3319.7118 643.14189 -3962.8537 733.15066 27034.087 -31733.898 298.01212 -335.68221 0.97040794 0.8375 -0.201 0.05025
1680000 -3282.2367 648.60366 -3930.8403 697.80758 27106.979 -31737.678 300.54294 -821.93638 0.97624892 0.84 -0.2016 0.0504
1685000 -3349.7097 610.17553 -3959.8852 714.2204 27061.577 -31739.049 282.73653 -608.03338 0.97715725 0.8425 -0.2022 0.05055
1690000 -3276.8907 654.19286 -3931.0836 753.31199 27051.143 -31737.814 303.1328 470.52169 1.0040827 0.845 -0.2028 0.0507
1695000 -3356.5028 624.6713 -3981.1741 721.8757 27033.813 -31738.204 289.45342 -594.09001 0.98851274 0.8475 -0.2034 0.05085
1700000 -3323.8154 626.79844 -3950.6138 744.24997 27041.346 -31738.556 290.43907 24.956241 0.98825494 0.85 -0.204 0.051
1705000 -3242.9786 679.9754 -3922.954 654.28813 27159.104 -31738.27 315.07963 -1251.9879 0.99005714 0.8525 -0.2046 0.05115
1710000 -3311.427 658.82294 -3970.25 721.93221 27043.021 -31738.466 305.27824 -621.60252 0.99919856 0.855 -0.2052 0.0513
1715000 -3321.1662 654.12092 -3975.2871 748.1525 27013.147 -31738.133 303.09946 199.42662 0.98584932 0.8575 -0.2058 0.05145
1720000 -3252.9739 630.37518 -3883.3491 764.34959 27086.819 -31735.934 292.09642 590.47908 0.96914932 0.86 -0.2064 0.0516
1725000 -3355.7913 629.38324 -3985.1745 773.89334 26977.905 -31738.013 291.63679 424.70863 0.98894849 0.8625 -0.207 0.05175
1730000 -3265.7677 679.33001 -3945.0977 741.70993 27044.967 -31735.714 314.78058 -156.32001 0.96682119 0.865 -0.2076 0.0519
1735000 -3329.3178 631.04003 -3960.3579 728.61842 27044.399 -31735.951 292.40449 -617.28914 0.9779626 0.8675 -0.2082 0.05205
1740000 -3276.4172 652.18346 -3928.6006 711.76567 27095.339 -31737.13 302.20171 -608.64098 0.97577767 0.87 -0.2088 0.0522
1745000 -3367.0629 619.23699 -3986.2999 714.70504 27034.572 -31738.184 286.93533 -881.7967 0.98850571 0.8725 -0.2094 0.05235
1750000 -3350.0569 625.65732 -3975.7142 730.88885 27025.633 -31734.804 289.91031 -297.14279 0.9893824 0.875 -0.21 0.0525
1755000 -3338.301 633.65415 -3971.9552 775.28876 26985.334 -31736.591 293.61579 412.3181 0.98557765 0.8775 -0.2106 0.05265
1760000 -3251.9064 667.70039 -3919.6068 795.48855 27019.487 -31738.029 309.39177 1649.3602 0.99301618 0.88 -0.2112 0.0528
1765000 -3297.0745 627.67022 -3924.7447 770.52235 27039.901 -31737.82 290.84303 857.08221 1.0083534 0.8825 -0.2118 0.05295
1770000 -3271.0779 654.10045 -3925.1783 728.58424 27081.992 -31739.013 303.08998 -88.428469 0.98111355 0.885 -0.2124 0.0531
1775000 -3346.407 605.46892 -3951.8759 742.13304 27039.004 -31735.678 280.55563 343.16771 0.99968234 0.8875 -0.213 0.05325
1780000 -3290.5326 661.67685 -3952.2094 760.33686 27023.324 -31738.767 306.60065 402.19944 0.99400686 0.89 -0.2136 0.0534
1785000 -3366.1206 638.40054 -4004.5211 751.36335 26975.592 -31735.746 295.81513 -269.13878 0.97165913 0.8925 -0.2142 0.05355
1790000 -3258.3055 622.65513 -3880.9606 676.40276 27176.903 -31736.935 288.51919 -830.57704 0.98709996 0.895 -0.2148 0.0537
1795000 -3312.0411 642.61352 -3954.6546 750.65851 27027.881 -31736.946 297.76729 340.63468 0.99666772 0.8975 -0.2154 0.05385
1800000 -3340.1029 629.50175 -3969.6047 755.54335 27008.136 -31736.646 291.6917 -362.32152 0.97026562 0.9 -0.216 0.054
1805000 -3239.5085 671.40118 -3910.9097 721.78691 27097.089 -31733.431 311.1066 110.04563 0.96382704 0.9025 -0.2166 0.05415
1810000 -3266.7865 684.65149 -3951.4379 757.10372 27027.29 -31737.399 317.24639 729.96782 1.0049447 0.905 -0.2172 0.0543
1815000 -3333.81 654.59809 -3988.4081 796.79491 26953.479 -31739.86 303.32057 730.60501 0.97490606 0.9075 -0.2178 0.05445
1820000 -3340.6271 615.49021 -3956.1173 771.71374 27012.552 -31741.723 285.19919 565.28134 0.98472964 0.91 -0.2184 0.0546
1825000 -3298.7504 643.65917 -3942.4095 724.49708 27069.231 -31738.213 298.25181 -298.62774 0.96726328 0.9125 -0.219 0.05475
1830000 -3290.9971 666.44583 -3957.443 668.19041 27111.858 -31739.915 308.81045 -1725.0885 0.97076205 0.915 -0.2196 0.0549
1835000 -3254.7179 677.57424 -3932.2922 726.00793 27078.89 -31740.472 313.96701 -300.48129 0.97472843 0.9175 -0.2202 0.05505
1840000 -3259.1244 703.38585 -3962.5102 754.37475 27017.218 -31737.576 325.92731 396.08403 0.99224318 0.92 -0.2208 0.0552
1845000 -3262.1107 624.81539 -3886.9261 719.208 27127.288 -31736.726 289.52019 205.96515 0.98538694 0.9225 -0.2214 0.05535
1850000 -3341.4941 642.35109 -3983.8452 753.00292 27001.459 -31740.126 297.64569 -115.99892 0.97327886 0.925 -0.222 0.0555
1855000 -3319.9831 602.04025 -3922.0234 742.3858 27073.567 -31741.193 278.96689 -7.4449495 0.98220359 0.9275 -0.2226 0.05565
1860000 -3306.9705 679.97559 -3986.9461 826.7132 26917.659 -31735.844 315.07972 995.54048 0.97137783 0.93 -0.2232 0.0558
1865000 -3293.9564 665.98336 -3959.9398 748.22311 27023.987 -31737.053 308.59616 726.98864 1.0142172 0.9325 -0.2238 0.05595
1870000 -3237.963 655.69966 -3893.6627 726.58511 27111.384 -31737.594 303.831 -21.727181 0.97281044 0.935 -0.2244 0.0561
1875000 -3374.6595 619.66759 -3994.3271 726.44658 27013.079 -31737.214 287.13485 -276.33824 1.0045608 0.9375 -0.225 0.05625
1880000 -3277.6826 660.5116 -3938.1942 744.90816 27048.289 -31732.964 306.06071 208.07192 0.98192071 0.94 -0.2256 0.0564
1885000 -3303.7764 641.96127 -3945.7377 700.82697 27086.5 -31737.254 297.46506 -705.0392 0.99500598 0.9425 -0.2262 0.05655
1890000 -3359.8447 609.89199 -3969.7367 700.20487 27066.841 -31738.549 282.60514 -713.02909 1.000895 0.945 -0.2268 0.0567
1895000 -3312.62 622.92578 -3935.5457 770.82145 27029.24 -31739.059 288.6446 1173.4526 1.0063156 0.9475 -0.2274 0.05685
1900000 -3308.4458 669.47072 -3977.9165 760.07479 26994.212 -31736.251 310.21209 -36.382368 0.97889335 0.95 -0.228 0.057
1905000 -3370.217 651.08853 -4021.3056 729.87681 26986.245 -31740.306 301.69435 -892.25427 0.98214988 0.9525 -0.2286 0.05715
1910000 -3297.6045 614.14852 -3911.753 725.77044 27099.174 -31739.96 284.57749 -123.36078 0.97752647 0.955 -0.2292 0.0573
1915000 -3292.1458 626.31854 -3918.4644 710.0067 27105.45 -31738.665 290.2167 -156.06234 0.98706768 0.9575 -0.2298 0.05745
1920000 -3258.6317 683.05625 -3941.688 733.15963 27058.48 -31737.899 316.50721 -331.27328 0.96792 0.96 -0.2304 0.0576
1925000 -3308.3003 643.25078 -3951.5511 734.71807 27042.131 -31733.678 298.06258 -899.10835 0.95191489 0.9625 -0.231 0.05775
1930000 -3275.685 662.2037 -3937.8887 716.74146 27078.527 -31736.562 306.84478 -54.012541 1.0043314 0.965 -0.2316 0.0579
1935000 -3287.9716 633.56371 -3921.5353 746.44129 27064.22 -31736.176 293.57389 1037.5548 1.0147673 0.9675 -0.2322 0.05805
1940000 -3250.1051 685.34381 -3935.4489 774.55817 27023.81 -31739.014 317.56719 1418.383 1.0125818 0.97 -0.2328 0.0582
1945000 -3270.0763 642.65027 -3912.7266 697.73057 27121.723 -31738.163 297.78432 -479.20715 0.98729311 0.9725 -0.2334 0.05835
1950000 -3334.5536 631.76366 -3966.3173 699.41626 27068.476 -31736.481 292.7398 -957.14355 0.97960776 0.975 -0.234 0.0585
1955000 -3276.8103 652.29988 -3929.1102 737.65435 27070.22 -31738.521 302.25565 262.50358 1.0038568 0.9775 -0.2346 0.05865
1960000 -3332.6922 636.66505 -3969.3573 705.90837 27055.869 -31736.072 295.01095 -833.658 0.97874229 0.98 -0.2352 0.0588
1965000 -3341.1449 667.15503 -4008.2999 810.06486 26919.746 -31741.042 309.13907 1144.3005 0.99581793 0.9825 -0.2358 0.05895
1970000 -3271.8283 655.42621 -3927.2545 789.31365 27019.023 -31737.916 303.7043 1151.1363 0.99225241 0.985 -0.2364 0.0591
1975000 -3300.0112 644.65396 -3944.6652 745.21042 27048.054 -31739.819 298.71277 136.49822 0.97832039 0.9875 -0.237 0.05925
1980000 -3335.2376 663.40445 -3998.642 758.8957 26979.416 -31739.34 307.40117 58.763635 0.9885575 0.99 -0.2376 0.0594
1985000 -3325.927 630.5991 -3956.5261 756.54904 27023.943 -31738.779 292.20018 85.287803 0.98050884 0.9925 -0.2382 0.05955
1990000 -3321.7443 646.44654 -3968.1909 721.63898 27049.911 -31741.98 299.54339 -748.66083 0.97438047 0.995 -0.2388 0.0597
1995000 -3330.3216 635.32254 -3965.6441 757.24268 27013.893 -31738.755 294.38888 174.06377 0.99429928 0.9975 -0.2394 0.05985
2000000 -3288.8004 648.87481 -3937.6752 759.37954 27037.886 -31738.632 300.66858 576.95398 0.9825578 1 -0.24 0.06
Loop time of 14266.5 on 12 procs for 2000000 steps with 1085 atoms
Performance: 12.112 ns/day, 1.981 hours/ns, 140.188 timesteps/s
97.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8600.4 | 9447.1 | 10304 | 431.3 | 66.22
Bond | 1.9552 | 2.2387 | 2.7546 | 17.1 | 0.02
Kspace | 2263.7 | 3114.5 | 3952 | 745.0 | 21.83
Neigh | 202.32 | 202.96 | 203.47 | 2.3 | 1.42
Comm | 561.5 | 621.86 | 650.82 | 123.8 | 4.36
Output | 0.087348 | 0.088453 | 0.095508 | 0.7 | 0.00
Modify | 610.45 | 680.28 | 833.73 | 327.1 | 4.77
Other | | 197.5 | | | 1.38
Nlocal: 90.4167 ave 96 max 82 min
Histogram: 1 0 1 1 1 1 2 2 1 2
Nghost: 3917.17 ave 3994 max 3861 min
Histogram: 3 0 3 0 1 1 1 2 0 1
Neighs: 0.833333 ave 4 max 0 min
Histogram: 8 0 1 0 0 1 0 1 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 80894
Dangerous builds = 0
unfix ADAPT
# perturb at lambda = 1 to 1.002
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
Setting atom values ...
1 settings made for charge
set type 2 charge 0.06
Setting atom values ...
4 settings made for charge
run 100000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.2855962
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014617012
estimated relative force accuracy = 4.4018698e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.17 | 12.19 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_q1 v_q2
2000000 -3288.972 648.87481 -3937.8468 759.21479 27022.033 -31722.786 300.66858 557.61728 0.9825578 0 -0 0
2005000 -3339.2403 630.84696 -3970.0873 808.35866 26939.504 -31721.357 292.31503 907.5228 0.95882444 0.05 -0.012 0.003
2010000 -3293.4357 644.38799 -3937.8236 743.29927 27035.504 -31720.895 298.58953 168.71632 1.0041513 0.1 -0.024 0.006
2015000 -3320.267 650.83038 -3971.0974 729.78096 27018.357 -31721.898 301.57473 -500.96868 0.97735764 0.15 -0.036 0.009
2020000 -3353.3442 603.27312 -3956.6174 690.54784 27068.222 -31720.143 279.53816 -894.15223 0.98189291 0.2 -0.048 0.012
2025000 -3325.3366 653.4454 -3978.782 715.4302 27022.62 -31721.301 302.78645 -462.9205 1.0051262 0.25 -0.06 0.015
2030000 -3310.4173 625.41253 -3935.8298 736.68056 27044.485 -31720.335 289.79688 282.8792 0.98868964 0.3 -0.072 0.018
2035000 -3261.9264 673.96414 -3935.8905 739.01684 27043.147 -31720.808 312.2942 111.678 0.98122086 0.35 -0.084 0.021
2040000 -3356.8739 644.80171 -4001.6756 742.40238 26973.989 -31722.377 298.78123 -432.84916 0.99466547 0.4 -0.096 0.024
2045000 -3346.3474 614.73882 -3961.0862 737.79499 27015.427 -31722.178 284.85102 -230.69328 0.97767956 0.45 -0.108 0.027
2050000 -3271.926 664.63446 -3936.5605 766.30428 27017.616 -31725.266 307.97112 998.48053 0.9955393 0.5 -0.12 0.03
2055000 -3270.5072 649.18665 -3919.6939 678.67195 27120.781 -31722.953 300.81308 -1392.9514 0.97326162 0.55 -0.132 0.033
2060000 -3313.667 664.12266 -3977.7896 712.65192 27027.826 -31722.699 307.73396 -587.7242 0.99650455 0.6 -0.144 0.036
2065000 -3289.8327 667.48259 -3957.3153 684.95638 27080.056 -31724.442 309.29085 -1094.5397 0.9863223 0.65 -0.156 0.039
2070000 -3306.2563 639.78827 -3946.0446 702.18722 27072.463 -31722.853 296.45816 -550.48807 0.9929239 0.7 -0.168 0.042
2075000 -3359.3025 627.51782 -3986.8203 788.08689 26945.752 -31723.619 290.77241 125.93028 0.97059845 0.75 -0.18 0.045
2080000 -3306.1412 624.55985 -3930.701 716.1404 27073.102 -31722.105 289.40178 -548.57976 0.98228358 0.8 -0.192 0.048
2085000 -3307.4737 624.2064 -3931.6801 733.09265 27051.745 -31719.08 289.238 -460.11479 0.97930419 0.85 -0.204 0.051
2090000 -3310.468 624.39901 -3934.867 707.99698 27076.658 -31722.288 289.32725 -888.29859 0.97434222 0.9 -0.216 0.054
2095000 -3377.8796 590.57499 -3968.4546 741.09769 27008.576 -31720.933 273.65424 118.93111 0.9965487 0.95 -0.228 0.057
2100000 -3314.2201 642.76946 -3956.9896 714.05716 27048.306 -31721.833 297.83955 -783.74719 0.96774087 1 -0.24 0.06
Loop time of 730.399 on 12 procs for 100000 steps with 1085 atoms
Performance: 11.829 ns/day, 2.029 hours/ns, 136.911 timesteps/s
97.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 466.74 | 500.8 | 530.72 | 82.2 | 68.56
Bond | 0.079647 | 0.11568 | 0.18656 | 10.0 | 0.02
Kspace | 112.2 | 141.66 | 175.29 | 152.7 | 19.39
Neigh | 10.36 | 10.384 | 10.414 | 0.5 | 1.42
Comm | 28.587 | 31.851 | 33.279 | 29.7 | 4.36
Output | 0.0046348 | 0.0046829 | 0.0050604 | 0.2 | 0.00
Modify | 31.173 | 35.093 | 43.611 | 79.4 | 4.80
Other | | 10.49 | | | 1.44
Nlocal: 90.4167 ave 104 max 83 min
Histogram: 5 1 0 0 0 4 1 0 0 1
Nghost: 3924.08 ave 3983 max 3859 min
Histogram: 1 0 1 2 2 1 1 3 0 1
Neighs: 0.833333 ave 10 max 0 min
Histogram: 11 0 0 0 0 0 0 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 4031
Dangerous builds = 0
# write_restart restart.*.lmp
write_data data.*.lmp
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28519655
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014841757
estimated relative force accuracy = 4.4695511e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Total wall time: 4:21:27

2736
examples/USER/fep/CH4hyd/fdti01/log.lammps
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23
examples/USER/fep/CH4hyd/fdti10/fdti10.fep Normal file
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@ -0,0 +1,23 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.00659904 10879.6 11000.7
200000 0.00581196 10894.3 11001
300000 0.00530381 10911.1 11008.5
400000 0.00475489 10897.5 10984.6
500000 0.0038383 10964 11034.6
600000 0.00310771 10922.8 10979.5
700000 0.00269436 10969 11018.3
800000 0.00176261 10975.4 11007.4
900000 0.0014834 10959.9 10986.7
1000000 -0.0011229 10980.5 10959
1100000 -0.00224922 10997.8 10955.3
1200000 -0.000865427 10992.1 10975.3
1300000 -0.00552223 11107.7 11002.9
1400000 -0.00744745 11156.9 11015.9
1500000 -0.0179421 11320.5 10979.5
1600000 -0.0194076 11310.1 10941.1
1700000 -0.0241497 11435.9 10977.5
1800000 -0.021435 11355.6 10952.8
1900000 -0.0136374 11220.2 10966
2000000 -0.00562975 11040.8 10936.9
2100000 -0.000386831 10936.6 10929.5

22
examples/USER/fep/CH4hyd/fdti10/fdti10.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.00671766 0.988799
200000 0.00591179 0.990139
300000 0.00495535 0.991733
400000 0.00428164 0.992859
500000 0.00367253 0.993879
600000 0.00334988 0.994424
700000 0.00246906 0.995908
800000 0.00139088 0.997725
900000 0.000491084 0.99924
1000000 0.000615407 0.999044
1100000 -0.00172714 1.00302
1200000 -0.00333962 1.00579
1300000 -0.0040424 1.00699
1400000 -0.0102385 1.01763
1500000 -0.0173611 1.03006
1600000 -0.0243837 1.04234
1700000 -0.0211518 1.03654
1800000 -0.0220119 1.03776
1900000 -0.013304 1.02261
2000000 -0.00648381 1.01095

31
examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp
View File

@ -41,7 +41,7 @@ timestep 1.0
velocity all create ${TK} 12345
thermo_style multi
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
@ -60,8 +60,8 @@ fix ADAPT all adapt/fep 100000 &
atom charge 2 v_q2 &
after yes
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal -0.002
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
@ -69,14 +69,33 @@ variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} &
pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2
atom charge 2 v_dq2 &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti10.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fdti10.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000
unfix ADAPT
# we don't want to evaluate the forward difference on the last point (lambda < 0)
# so we simulate at 0.002 and perturb to 0.0
variable lambda equal 0.002
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 ${lambda} # C4H Ow
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 ${lambda} # C4H Hw
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 ${lambda} # H Ow
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 ${lambda} # H Hw
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
set type 1 charge ${q1}
set type 2 charge ${q2}
run 100000
# write_restart restart.*.lmp
write_data data.*.lmp

810
examples/USER/fep/CH4hyd/fdti10/log.fdti10 Normal file
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@ -0,0 +1,810 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# created by fftool
print "Methane in TIP4P water"
Methane in TIP4P water
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.lmp
Reading data file ...
orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
2 by 2 by 3 MPI processor grid
reading atoms ...
1085 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
724 bonds
reading angles ...
366 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.015 seconds
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm/tip4p 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
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
variable TK equal 300.0
variable PBAR equal 1.0
fix SHAKE all shake 0.0001 20 0 b 2 a 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
360 = # of frozen angles
find clusters CPU = 0.000 seconds
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
velocity all create 300 12345
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 1 1000
run 100000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.27021504
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.025872736
estimated relative force accuracy = 7.7914976e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.87 | 10.88 | 10.90 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density
0 546.33019 647.43194 -101.10176 -205.36298 29920.627 -29816.534 300 788.91776 0.55642578
5000 -3293.7887 627.99038 -3921.7791 719.6947 25372.789 -30015.189 290.99138 -479.95734 0.9593797
10000 -3331.8077 662.98464 -3994.7923 713.75931 25307.342 -30018.317 307.20664 -898.12579 0.98999504
15000 -3301.0664 627.03645 -3928.1029 713.74138 25370.946 -30014.046 290.54936 -109.9857 0.99219341
20000 -3297.0753 653.68091 -3950.7562 690.09393 25371.803 -30016.409 302.89558 -1292.1349 0.97162179
25000 -3275.1265 686.51678 -3961.6433 721.21849 25332.103 -30016.791 318.11071 -782.2511 0.96262585
30000 -3319.4764 641.48819 -3960.9646 695.13846 25358.256 -30016.462 297.24585 -1032.3693 0.97723105
35000 -3339.5958 640.96354 -3980.5593 746.14675 25286.621 -30016.405 297.00274 -144.41371 0.99597619
40000 -3303.8432 650.4284 -3954.2716 763.59884 25292.808 -30013.426 301.38846 290.54097 0.97091267
45000 -3288.6614 644.14778 -3932.8092 738.75427 25339.802 -30013.275 298.47822 203.13743 0.98353192
50000 -3314.5145 647.31284 -3961.8273 734.66685 25319.659 -30017.097 299.94481 -575.98875 0.96495858
55000 -3325.2116 627.09779 -3952.3094 758.50764 25300.029 -30012.977 290.57778 115.22411 0.96610359
60000 -3279.2821 660.91919 -3940.2013 777.80296 25297.967 -30017.7 306.24957 512.56809 0.95818026
65000 -3348.4144 627.03753 -3975.4519 663.13879 25377.083 -30017.103 290.54986 -1659.0852 0.99578827
70000 -3217.4766 677.26277 -3894.7394 720.54024 25395.021 -30012.777 313.82269 375.82022 0.99971463
75000 -3281.149 677.15421 -3958.3032 733.96553 25322.666 -30016.859 313.77238 -255.76801 0.98119917
80000 -3305.1444 657.51092 -3962.6553 791.41752 25259.267 -30014.718 304.67029 1173.0658 0.99379829
85000 -3304.8727 630.4153 -3935.288 735.79644 25341.978 -30016.371 292.11501 -267.42267 0.96149675
90000 -3300.5216 656.36473 -3956.8864 760.14613 25296.025 -30017.438 304.13918 414.5575 0.98279507
95000 -3278.8725 650.70078 -3929.5733 716.16787 25367.048 -30014.72 301.51468 -390.98983 0.97417615
100000 -3294.7866 648.37071 -3943.1573 689.04498 25379.449 -30013.819 300.435 -1095.9528 0.98149922
Loop time of 688.088 on 12 procs for 100000 steps with 1085 atoms
Performance: 12.557 ns/day, 1.911 hours/ns, 145.330 timesteps/s
96.8% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 435.35 | 459.62 | 497.98 | 84.0 | 66.80
Bond | 0.082101 | 0.11327 | 0.23061 | 13.2 | 0.02
Kspace | 102.86 | 141.29 | 165.76 | 151.4 | 20.53
Neigh | 10.332 | 10.355 | 10.376 | 0.5 | 1.50
Comm | 28.944 | 31.778 | 33.101 | 28.5 | 4.62
Output | 0.0012362 | 0.0012819 | 0.0017332 | 0.4 | 0.00
Modify | 31.988 | 35.926 | 44.057 | 76.2 | 5.22
Other | | 9.009 | | | 1.31
Nlocal: 90.4167 ave 100 max 78 min
Histogram: 1 0 0 3 1 2 0 1 2 2
Nghost: 3899.33 ave 3973 max 3848 min
Histogram: 2 1 2 2 1 0 2 0 0 2
Neighs: 0.833333 ave 10 max 0 min
Histogram: 11 0 0 0 0 0 0 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 4057
Dangerous builds = 1
reset_timestep 0
variable lambda equal ramp(1.0,0.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix ADAPT all adapt/fep 100000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda atom charge 1 v_q1 atom charge 2 v_q2 after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal -0.002
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
compute FEP all fep 300 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fdti10.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28556787
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014632842
estimated relative force accuracy = 4.4066369e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
FEP settings ...
temperature = 300.000000
tail no
lj/cut/tip4p/long/soft lambda 1-2 3-4
1-1 charge
2-2 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.17 | 12.18 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_q1 v_q2
0 -3294.6922 648.37071 -3943.0629 689.04498 27082.786 -31717.062 300.435 -1136.6197 0.98149922 1 -0.24 0.06
5000 -3300.0855 688.75259 -3988.8381 720.09187 27007.194 -31718.806 319.14672 -490.2005 0.99596885 0.9975 -0.2394 0.05985
10000 -3331.4444 652.57047 -3984.0149 770.13024 26964.178 -31720.156 302.38103 608.19798 0.9867963 0.995 -0.2388 0.0597
15000 -3317.9366 623.85905 -3941.7956 734.96511 27038.729 -31718.813 289.07705 -68.894551 0.99620066 0.9925 -0.2382 0.05955
20000 -3356.5017 622.48112 -3978.9828 791.34687 26946.421 -31718.414 288.43856 347.88492 0.95690123 0.99 -0.2376 0.0594
25000 -3308.6241 637.21901 -3945.8432 701.68867 27069.809 -31719.744 295.26764 -576.40592 0.97808938 0.9875 -0.237 0.05925
30000 -3268.9616 646.30182 -3915.2635 692.86607 27107.067 -31719.486 299.47633 -627.1163 0.98270296 0.985 -0.2364 0.0591
35000 -3353.5791 627.44774 -3981.0268 715.64502 27018.484 -31720.596 290.73993 -671.96581 0.97562727 0.9825 -0.2358 0.05895
40000 -3366.3894 615.13583 -3981.5252 739.84021 26993.162 -31717.781 285.03498 71.956237 1.0028711 0.98 -0.2352 0.0588
45000 -3278.7772 653.03561 -3931.8128 728.3238 27058.386 -31720.847 302.59657 -204.57499 0.98355616 0.9775 -0.2346 0.05865
50000 -3328.0409 652.01796 -3980.0589 735.50885 26999.996 -31717.026 302.12502 -147.36813 0.99832388 0.975 -0.234 0.0585
55000 -3320.7332 634.51016 -3955.2434 733.31216 27030.192 -31720.582 294.01245 -214.13289 0.97804272 0.9725 -0.2334 0.05835
60000 -3265.0127 649.66719 -3914.6799 717.71007 27084.95 -31719.395 301.03574 -275.84112 0.97721238 0.97 -0.2328 0.0582
65000 -3296.9453 667.09895 -3964.0443 713.15355 27038.116 -31717.446 309.11308 -775.40143 0.9596487 0.9675 -0.2322 0.05805
70000 -3326.8176 610.1396 -3936.9572 759.12327 27019.426 -31720.267 282.71988 386.9984 0.9805237 0.965 -0.2316 0.0579
75000 -3295.6213 619.43931 -3915.0606 744.41867 27057.616 -31720.379 287.02908 160.31549 0.96526127 0.9625 -0.231 0.05775
80000 -3319.0003 642.16787 -3961.1682 698.26556 27056.473 -31718.957 297.56079 -812.57812 0.97915775 0.96 -0.2304 0.0576
85000 -3275.3452 671.73859 -3947.0838 734.53053 27033.862 -31718.806 311.26295 555.74464 1.0247379 0.9575 -0.2298 0.05745
90000 -3353.1322 603.88322 -3957.0155 762.05179 26995.621 -31717.378 279.82086 84.455754 0.97122429 0.955 -0.2292 0.0573
95000 -3310.0949 630.02684 -3940.1218 661.29743 27115.782 -31720.067 291.93501 -1117.7295 0.99837384 0.9525 -0.2286 0.05715
100000 -3287.7733 633.81565 -3921.5889 687.00844 27108.543 -31719.948 293.69063 -1082.8287 0.97122457 0.95 -0.228 0.057
105000 -3320.9973 642.25999 -3963.2573 771.15562 26984.002 -31720.37 297.60348 494.27724 0.97939567 0.9475 -0.2274 0.05685
110000 -3271.2503 682.46763 -3953.7179 717.72459 27040.506 -31715.648 316.23446 139.98334 1.0061057 0.945 -0.2268 0.0567
115000 -3230.6271 657.8128 -3888.4399 704.94943 27121.81 -31718.884 304.81017 -175.18562 0.98938679 0.9425 -0.2262 0.05655
120000 -3354.4761 646.55896 -4001.0351 737.80008 26979.08 -31719.117 299.59549 -687.78242 0.97356203 0.94 -0.2256 0.0564
125000 -3307.9326 651.94271 -3959.8753 767.93628 26986.225 -31715.772 302.09015 674.48659 0.99075217 0.9375 -0.225 0.05625
130000 -3252.6616 653.33949 -3906.0011 737.70688 27069.103 -31715.61 302.73737 61.502238 0.95074576 0.935 -0.2244 0.0561
135000 -3337.2068 624.11194 -3961.3188 726.10143 27027.534 -31718.691 289.19423 -399.06739 0.975193 0.9325 -0.2238 0.05595
140000 -3273.2993 650.03446 -3923.3337 722.58849 27068.141 -31718.93 301.20593 109.7555 1.0125164 0.93 -0.2232 0.0558
145000 -3361.1844 630.1629 -3991.3473 761.22674 26960.945 -31717.903 291.99806 98.529698 0.9842552 0.9275 -0.2226 0.05565
150000 -3397.6956 620.04439 -4017.74 769.23302 26927.291 -31716.976 287.30945 -4.6260994 0.98671248 0.925 -0.222 0.0555
155000 -3324.2698 633.84999 -3958.1198 762.57412 26996.897 -31721.318 293.70654 548.34435 0.98920982 0.9225 -0.2214 0.05535
160000 -3343.9484 643.52355 -3987.4719 759.58357 26968.943 -31717.703 298.18897 -14.622864 0.98634427 0.92 -0.2208 0.0552
165000 -3312.27 638.38126 -3950.6513 734.66797 27029.589 -31718.628 295.80619 -278.68476 0.97131029 0.9175 -0.2202 0.05505
170000 -3304.1638 653.71924 -3957.883 758.71859 26998.407 -31717.699 302.91334 556.6553 0.99062914 0.915 -0.2196 0.0549
175000 -3348.5751 636.35096 -3984.926 716.66884 27013.923 -31719.395 294.86542 -493.93923 1.0094499 0.9125 -0.219 0.05475
180000 -3314.3089 642.35345 -3956.6623 746.03994 27014.289 -31719.309 297.64678 18.793089 0.98688216 0.91 -0.2184 0.0546
185000 -3305.5307 656.49472 -3962.0254 698.68453 27053.976 -31718.699 304.19941 -655.04866 0.9953262 0.9075 -0.2178 0.05445
190000 -3319.0075 628.14762 -3947.1551 760.10501 27010.832 -31719.877 291.06424 495.59849 0.99024489 0.905 -0.2172 0.0543
195000 -3359.1251 645.3591 -4004.4842 706.03177 27003.968 -31717.297 299.03951 -987.2232 1.0030744 0.9025 -0.2166 0.05415
200000 -3265.1994 653.17314 -3918.3725 745.43252 27051.185 -31716.468 302.66029 492.87431 0.98271789 0.9 -0.216 0.054
205000 -3326.7435 634.62415 -3961.3677 733.67518 27021.402 -31718.37 294.06526 -610.98205 0.97647098 0.8975 -0.2154 0.05385
210000 -3341.4069 629.61701 -3971.0239 788.26956 26951.424 -31717.953 291.74511 784.09039 0.98181574 0.895 -0.2148 0.0537
215000 -3328.6327 629.18147 -3957.8142 741.68875 27018.252 -31720.903 291.54329 -389.24921 0.97384889 0.8925 -0.2142 0.05355
220000 -3330.2335 631.1408 -3961.3743 711.41512 27041.269 -31717.027 292.45119 -529.07456 0.99951453 0.89 -0.2136 0.0534
225000 -3279.1467 651.38387 -3930.5306 675.7848 27109.317 -31717.64 301.8312 -1355.4842 0.97063846 0.8875 -0.213 0.05325
230000 -3258.5618 674.19802 -3932.7598 696.46848 27086.441 -31719.629 312.40257 -798.15463 0.98875283 0.885 -0.2124 0.0531
235000 -3301.5452 661.5648 -3963.11 760.55878 26993.336 -31718.61 306.54873 388.65302 0.98559781 0.8825 -0.2118 0.05295
240000 -3260.292 688.11931 -3948.4113 796.99706 26969.933 -31716.82 318.85327 1273.6638 0.98971045 0.88 -0.2112 0.0528
245000 -3335.2668 650.00152 -3985.2683 732.51438 26997.569 -31719.222 301.19066 -527.33325 0.97446562 0.8775 -0.2106 0.05265
250000 -3335.3004 634.43787 -3969.7383 693.40008 27051.388 -31715.921 293.97895 -775.65835 0.997393 0.875 -0.21 0.0525
255000 -3308.9727 644.64293 -3953.6156 775.97061 26985.278 -31718.351 298.70766 735.72268 0.97151151 0.8725 -0.2094 0.05235
260000 -3377.5078 607.25295 -3984.7607 756.34352 26972.957 -31717.896 281.3823 421.20354 0.99480934 0.87 -0.2088 0.0522
265000 -3332.2782 635.01747 -3967.2957 774.98012 26971.131 -31718.281 294.24751 542.48287 0.9953591 0.8675 -0.2082 0.05205
270000 -3300.1877 666.69132 -3966.879 740.28005 27005.011 -31716.98 308.9242 324.45834 1.010532 0.865 -0.2076 0.0519
275000 -3310.6523 656.2584 -3966.9107 742.16026 27009.436 -31720.438 304.08991 -39.601026 0.99637116 0.8625 -0.207 0.05175
280000 -3267.8018 673.29725 -3941.0991 718.41223 27057.428 -31719.711 311.98519 -199.35683 0.99136443 0.86 -0.2064 0.0516
285000 -3331.8267 646.80574 -3978.6324 741.20142 26993.85 -31717.481 299.70984 -196.98987 0.98711039 0.8575 -0.2058 0.05145
290000 -3290.9098 646.64126 -3937.551 712.52482 27064.101 -31718.746 299.63362 -716.1483 0.9903895 0.855 -0.2052 0.0513
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1590000 -3308.4639 639.37584 -3947.8397 743.30005 27020.978 -31714.363 296.26705 -279.73715 0.97484698 0.205 -0.0492 0.0123
1595000 -3329.8877 649.55812 -3979.4458 702.84384 27032.069 -31716.36 300.98521 -1510.2883 0.97678091 0.2025 -0.0486 0.01215
1600000 -3292.354 662.27897 -3954.6329 775.40332 26984.964 -31717.39 306.87965 673.81116 0.9855796 0.2 -0.048 0.012
1605000 -3315.4101 629.98766 -3945.3977 717.94159 27048.515 -31713.143 291.91686 -301.8112 1.0009264 0.1975 -0.0474 0.01185
1610000 -3275.4657 658.57092 -3934.0366 715.95346 27057.985 -31710.751 305.16146 -603.47656 0.96953792 0.195 -0.0468 0.0117
1615000 -3285.5868 666.64007 -3952.2269 756.05821 27008.457 -31718.765 308.90045 330.55017 0.98556768 0.1925 -0.0462 0.01155
1620000 -3317.8609 640.24033 -3958.1012 752.94113 27000.029 -31713.803 296.66763 379.89085 0.98657781 0.19 -0.0456 0.0114
1625000 -3329.9371 624.91323 -3954.8503 686.10256 27073.07 -31715.906 289.56552 -1035.1056 0.99966536 0.1875 -0.045 0.01125
1630000 -3301.835 650.82574 -3952.6607 777.5543 26982.974 -31716.033 301.57258 1016.492 0.99648451 0.185 -0.0444 0.0111
1635000 -3296.4415 640.54523 -3936.9868 735.4715 27037.521 -31712.297 296.80891 -318.40304 0.97775334 0.1825 -0.0438 0.01095
1640000 -3310.2176 666.27575 -3976.4934 734.21075 27003.816 -31716.482 308.73164 -474.96967 0.99005044 0.18 -0.0432 0.0108
1645000 -3327.5225 647.73326 -3975.2557 772.36961 26966.417 -31716.081 300.13962 58.624678 0.96587474 0.1775 -0.0426 0.01065
1650000 -3321.3309 649.53534 -3970.8662 777.01324 26966.538 -31717.763 300.97465 108.71811 0.977065 0.175 -0.042 0.0105
1655000 -3403.4099 624.4219 -4027.8318 784.1127 26901.103 -31715.332 289.33786 68.508642 0.98072121 0.1725 -0.0414 0.01035
1660000 -3322.9984 664.06939 -3987.0678 731.71583 26995.436 -31716.834 307.70928 -332.14967 1.0025238 0.17 -0.0408 0.0102
1665000 -3230.6744 674.72794 -3905.4023 778.68595 27028.003 -31714.516 312.64812 1375.7415 0.99106584 0.1675 -0.0402 0.01005
1670000 -3290.79 637.69021 -3928.4802 700.32081 27081.091 -31712.466 295.48598 -1069.0971 0.96641143 0.165 -0.0396 0.0099
1675000 -3305.5875 621.22384 -3926.8113 695.99742 27090.166 -31715.288 287.85597 -1077.693 0.97177543 0.1625 -0.039 0.00975
1680000 -3268.9563 666.32635 -3935.2826 731.88233 27044.222 -31713.791 308.75509 -292.28331 0.97523238 0.16 -0.0384 0.0096
1685000 -3265.1149 639.41443 -3904.5293 721.62746 27086.503 -31716.035 296.28493 128.76044 0.99772509 0.1575 -0.0378 0.00945
1690000 -3326.8204 620.81306 -3947.6335 711.91766 27051.866 -31714.515 287.66563 -454.38876 0.98740179 0.155 -0.0372 0.0093
1695000 -3323.3897 684.06584 -4007.4555 744.82803 26961.661 -31715.201 316.97502 -679.14465 0.98094411 0.1525 -0.0366 0.00915
1700000 -3294.5706 653.01083 -3947.5814 781.85245 26983.199 -31713.887 302.58508 502.73081 0.97555506 0.15 -0.036 0.009
1705000 -3262.6576 685.19558 -3947.8532 757.26837 27012.265 -31718.135 317.49851 199.86853 0.97458873 0.1475 -0.0354 0.00885
1710000 -3255.8527 664.21235 -3920.065 703.16733 27091.894 -31717.024 307.77552 -355.94123 0.98084795 0.145 -0.0348 0.0087
1715000 -3287.5581 663.07942 -3950.6375 745.7211 27017.25 -31716.816 307.25056 114.0679 0.98657314 0.1425 -0.0342 0.00855
1720000 -3288.8458 658.50053 -3947.3463 690.29419 27077.889 -31717.344 305.12884 -1077.3116 0.98627147 0.14 -0.0336 0.0084
1725000 -3256.8223 656.34601 -3913.1683 768.47754 27032.602 -31715.721 304.1305 1023.5837 1.0029652 0.1375 -0.033 0.00825
1730000 -3346.7551 634.38611 -3981.1412 787.69666 26941.51 -31713.373 293.95496 464.32109 1.0083983 0.135 -0.0324 0.0081
1735000 -3294.4857 631.50013 -3925.9858 797.15264 26989.537 -31715.081 292.61769 835.64006 0.97238705 0.1325 -0.0318 0.00795
1740000 -3277.7412 645.9919 -3923.7331 727.45728 27061.304 -31714.776 299.33273 250.78941 0.9991219 0.13 -0.0312 0.0078
1745000 -3197.3765 716.79028 -3914.1668 734.244 27064.614 -31716.712 332.13851 19.166712 0.98333244 0.1275 -0.0306 0.00765
1750000 -3280.6313 622.07639 -3902.7076 700.86328 27106.933 -31712.398 288.25102 -658.71601 0.96809002 0.125 -0.03 0.0075
1755000 -3353.4925 658.66227 -4012.1548 757.72466 26942.913 -31715.245 305.20379 -343.411 0.98054785 0.1225 -0.0294 0.00735
1760000 -3269.008 691.45617 -3960.4641 748.05619 27002.818 -31713.225 320.39947 -167.78778 0.9720822 0.12 -0.0288 0.0072
1765000 -3312.1326 611.95973 -3924.0924 757.47097 27030.715 -31714.571 283.56327 594.93622 0.99970232 0.1175 -0.0282 0.00705
1770000 -3286.3959 628.16202 -3914.5579 717.36235 27083.618 -31717.665 291.07091 -696.94933 0.96376643 0.115 -0.0276 0.0069
1775000 -3349.2898 646.78418 -3996.0739 788.07114 26929.998 -31716.612 299.69985 582.27147 0.99837139 0.1125 -0.027 0.00675
1780000 -3347.1791 641.46049 -3988.6396 771.25773 26949.128 -31712.171 297.23301 78.03711 0.98201965 0.11 -0.0264 0.0066
1785000 -3399.4313 609.86503 -4009.2964 774.22094 26930.236 -31715.572 282.59265 18.158627 0.99130491 0.1075 -0.0258 0.00645
1790000 -3256.2797 680.01538 -3936.2951 772.26827 27002.742 -31713.66 315.09816 310.40267 0.97426571 0.105 -0.0252 0.0063
1795000 -3235.4884 688.93945 -3924.4278 732.98748 27057.009 -31716.446 319.2333 331.09084 1.0121548 0.1025 -0.0246 0.00615
1800000 -3219.9708 706.2187 -3926.1895 718.33138 27063.848 -31711.164 327.23997 -296.07765 0.98975934 0.1 -0.024 0.006
1805000 -3347.4225 630.49902 -3977.9215 790.79036 26943.342 -31714.525 292.15381 806.57337 0.98493764 0.0975 -0.0234 0.00585
1810000 -3316.95 672.66189 -3989.6119 701.96639 27021.379 -31715.012 311.69078 -1055.3668 0.98445711 0.095 -0.0228 0.0057
1815000 -3271.6474 640.25549 -3911.9029 731.4301 27070.097 -31714.358 296.67465 235.37666 1.0034769 0.0925 -0.0222 0.00555
1820000 -3268.5852 680.254 -3948.8392 698.09264 27066.868 -31716.458 315.20873 -1109.4344 0.96597756 0.09 -0.0216 0.0054
1825000 -3262.9465 630.22321 -3893.1697 726.12284 27094.819 -31716.584 292.026 581.49063 1.0165405 0.0875 -0.021 0.00525
1830000 -3325.4078 638.0573 -3963.4651 756.40841 26993.12 -31714.702 295.65608 457.52139 1.0060574 0.085 -0.0204 0.0051
1835000 -3290.2308 674.15556 -3964.3864 765.51879 26983.211 -31715.658 312.3829 413.34394 0.99030238 0.0825 -0.0198 0.00495
1840000 -3293.6063 667.63971 -3961.246 762.12518 26989.509 -31714.815 309.36366 251.72168 0.98152944 0.08 -0.0192 0.0048
1845000 -3284.2343 648.29591 -3932.5302 699.15751 27081.807 -31715.665 300.40034 -775.34257 0.98697792 0.0775 -0.0186 0.00465
1850000 -3318.1752 650.0401 -3968.2153 754.30022 26990.44 -31715.971 301.20854 31.798924 0.99366234 0.075 -0.018 0.0045
1855000 -3306.6157 643.15276 -3949.7685 706.55721 27057.479 -31715.55 298.01716 -517.28002 1.0016605 0.0725 -0.0174 0.00435
1860000 -3338.5777 667.1098 -4005.6875 791.29942 26914.244 -31714.244 309.11811 255.63501 0.9776517 0.07 -0.0168 0.0042
1865000 -3255.8144 682.49145 -3938.3059 787.02607 26989.795 -31716.255 316.24549 1264.0634 0.99887736 0.0675 -0.0162 0.00405
1870000 -3252.5858 652.25726 -3904.843 728.41299 27078.64 -31714.713 302.2359 -144.5641 0.96491991 0.065 -0.0156 0.0039
1875000 -3309.5832 657.30055 -3966.8837 757.25255 26988.913 -31716.067 304.57281 -98.604822 0.97743277 0.0625 -0.015 0.00375
1880000 -3291.493 627.19859 -3918.6916 813.07962 26981.192 -31715.581 290.62449 1806.5676 0.99104762 0.06 -0.0144 0.0036
1885000 -3281.941 687.05046 -3968.9915 763.18602 26982.454 -31716.979 318.358 417.67646 0.98625193 0.0575 -0.0138 0.00345
1890000 -3341.5498 656.97914 -3998.5289 745.15547 26970.163 -31715.423 304.42388 -504.08068 0.98243229 0.055 -0.0132 0.0033
1895000 -3301.6893 646.54019 -3948.2295 755.23573 27006.885 -31712.598 299.58679 376.14539 1.0048319 0.0525 -0.0126 0.00315
1900000 -3311.333 679.67795 -3991.011 789.29593 26931.648 -31715.122 314.9418 1037.345 1.0008807 0.05 -0.012 0.003
1905000 -3272.5003 668.40254 -3940.9029 718.08609 27055.948 -31716.781 309.71713 -286.48891 0.9881103 0.0475 -0.0114 0.00285
1910000 -3316.0584 632.02506 -3948.0835 717.60788 27049.658 -31715.89 292.86092 -677.83531 0.97723045 0.045 -0.0108 0.0027
1915000 -3290.6575 648.69049 -3939.348 758.99479 27016.633 -31716.858 300.58317 246.76601 0.96014992 0.0425 -0.0102 0.00255
1920000 -3337.0208 654.36708 -3991.3879 778.3941 26944.246 -31716.56 303.21353 139.89699 0.97481392 0.04 -0.0096 0.0024
1925000 -3308.835 651.31942 -3960.1544 747.1061 27005.987 -31715.946 301.80134 198.017 1.0050256 0.0375 -0.009 0.00225
1930000 -3267.2823 650.37412 -3917.6564 687.99454 27106.599 -31714.928 301.36332 -1038.4201 1.0011545 0.035 -0.0084 0.0021
1935000 -3236.5517 660.79742 -3897.3492 735.17944 27080.865 -31714.98 306.19315 447.84091 0.98014234 0.0325 -0.0078 0.00195
1940000 -3302.0749 666.44585 -3968.5207 714.39673 27032.752 -31716.425 308.81046 -473.87926 0.99447376 0.03 -0.0072 0.0018
1945000 -3289.2027 649.86308 -3939.0658 768.49924 27007.675 -31717.121 301.12651 762.21746 0.99009954 0.0275 -0.0066 0.00165
1950000 -3302.329 674.76941 -3977.0984 747.09562 26989.466 -31715.313 312.66734 54.832799 0.98726677 0.025 -0.006 0.0015
1955000 -3374.3031 630.83296 -4005.136 748.81361 26958.785 -31714.835 292.30855 -55.126833 1.0060118 0.0225 -0.0054 0.00135
1960000 -3310.8401 650.42767 -3961.2678 698.49943 27052.7 -31715.642 301.38813 -934.48079 0.99288724 0.02 -0.0048 0.0012
1965000 -3322.5064 642.37053 -3964.8769 716.05096 27034.95 -31717.88 297.6547 -665.83966 0.99509011 0.0175 -0.0042 0.00105
1970000 -3342.4338 651.08011 -3993.5139 736.17906 26984.325 -31715.44 301.69045 -270.5898 1.0014792 0.015 -0.0036 0.0009
1975000 -3214.2892 674.99303 -3889.2823 709.11194 27114.071 -31714.739 312.77096 -484.54747 0.97382166 0.0125 -0.003 0.00075
1980000 -3295.588 655.21711 -3950.8051 774.69267 26985.789 -31714.898 303.60741 87.748457 0.97621381 0.01 -0.0024 0.0006
1985000 -3294.657 629.82765 -3924.4846 768.55597 27021.837 -31717.283 291.84272 954.88617 1.0050703 0.0075 -0.0018 0.00045
1990000 -3257.912 660.54527 -3918.4573 722.75762 27072.838 -31716.199 306.07631 -423.44025 0.97598965 0.005 -0.0012 0.0003
1995000 -3329.3158 619.57927 -3948.8951 741.75692 27023.601 -31715.502 287.09393 82.743609 0.98909553 0.0025 -0.0006 0.00015
2000000 -3319.1334 640.84972 -3959.9831 743.80101 27008.342 -31715.397 296.95 -195.97682 0.9873309 0 -0 0
Loop time of 14386.5 on 12 procs for 2000000 steps with 1085 atoms
Performance: 12.011 ns/day, 1.998 hours/ns, 139.019 timesteps/s
97.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8939.1 | 9597.8 | 10349 | 389.2 | 66.71
Bond | 1.9775 | 2.2715 | 2.7731 | 13.6 | 0.02
Kspace | 2301.1 | 3048.8 | 3700.5 | 686.9 | 21.19
Neigh | 203.77 | 204.32 | 204.78 | 2.4 | 1.42
Comm | 578.49 | 636.33 | 664.79 | 122.0 | 4.42
Output | 0.088503 | 0.089486 | 0.096517 | 0.7 | 0.00
Modify | 626.56 | 700.4 | 854.45 | 325.4 | 4.87
Other | | 196.4 | | | 1.37
Nlocal: 90.4167 ave 102 max 80 min
Histogram: 1 2 0 3 0 2 1 1 1 1
Nghost: 3928.08 ave 3982 max 3886 min
Histogram: 2 1 2 1 1 1 2 0 0 2
Neighs: 0.833333 ave 9 max 0 min
Histogram: 10 1 0 0 0 0 0 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 80758
Dangerous builds = 0
unfix ADAPT
# we don't want to evaluate the forward difference on the last point (lambda < 0)
# so we simulate at 0.002 and perturb to 0.0
variable lambda equal 0.002
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 ${lambda} # C4H Ow
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 0.002
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 ${lambda} # C4H Hw
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.002
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 ${lambda} # H Ow
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.002
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 ${lambda} # H Hw
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.002
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
set type 1 charge ${q1}
set type 1 charge -0.00048
Setting atom values ...
1 settings made for charge
set type 2 charge ${q2}
set type 2 charge 0.00012
Setting atom values ...
4 settings made for charge
run 100000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28572351
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014544297
estimated relative force accuracy = 4.3799718e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.17 | 12.19 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_q1 v_q2
2000000 -3319.1328 640.84972 -3959.9825 743.79732 27025.601 -31732.651 296.95 -153.27227 0.9873309 0.002 -0.00048 0.00012
2005000 -3283.8996 685.33413 -3969.2337 764.928 26993.84 -31730.689 317.5627 225.99264 0.97794586 0.002 -0.00048 0.00012
2010000 -3227.9075 692.45046 -3920.3579 798.82986 27008.309 -31729.352 320.86019 1561.2012 0.99509268 0.002 -0.00048 0.00012
2015000 -3255.238 668.8117 -3924.0497 753.37151 27054.962 -31734.297 309.90672 407.50637 0.99083174 0.002 -0.00048 0.00012
2020000 -3340.1741 625.58467 -3965.7587 710.42424 27052.685 -31731.31 289.87665 -979.40495 0.98006179 0.002 -0.00048 0.00012
2025000 -3350.103 639.39311 -3989.4961 744.84072 26996.29 -31733.423 296.27505 -296.42087 0.99515417 0.002 -0.00048 0.00012
2030000 -3288.7885 657.77484 -3946.5633 753.00498 27027.542 -31729.781 304.79258 264.89611 0.9951047 0.002 -0.00048 0.00012
2035000 -3261.5263 667.85244 -3929.3787 719.06031 27082.814 -31733.01 309.46223 -280.77376 0.98490386 0.002 -0.00048 0.00012
2040000 -3316.5843 633.08448 -3949.6688 767.42405 27013.876 -31733.03 293.35183 816.43931 1.0050073 0.002 -0.00048 0.00012
2045000 -3352.3827 636.19373 -3988.5764 730.4996 27013.807 -31734.426 294.79256 -543.47035 0.98951055 0.002 -0.00048 0.00012
2050000 -3238.0335 658.23704 -3896.2705 653.08945 27184.713 -31736.008 305.00675 -1029.0772 0.9934289 0.002 -0.00048 0.00012
2055000 -3274.7515 657.54245 -3932.2939 737.73204 27060.292 -31732.359 304.6849 -195.91627 0.9670004 0.002 -0.00048 0.00012
2060000 -3371.8161 616.58527 -3988.4014 794.03472 26948.692 -31733.986 285.7066 639.16124 0.98880156 0.002 -0.00048 0.00012
2065000 -3298.1579 639.17893 -3937.3369 712.31161 27080.323 -31732.063 296.17581 -732.97393 0.97558207 0.002 -0.00048 0.00012
2070000 -3282.1355 637.68976 -3919.8253 659.11964 27150.124 -31731.592 295.48577 -1430.5926 0.98912072 0.002 -0.00048 0.00012
2075000 -3323.0139 645.70249 -3968.7164 671.66928 27088.865 -31730.74 299.19863 -1462.3479 0.99867179 0.002 -0.00048 0.00012
2080000 -3335.7423 628.95934 -3964.7016 753.12081 27012.893 -31732.278 291.44036 148.03744 1.0018533 0.002 -0.00048 0.00012
2085000 -3288.8582 643.18974 -3932.0479 756.71452 27039.719 -31730.657 298.03429 704.64446 1.0067855 0.002 -0.00048 0.00012
2090000 -3329.7017 657.07256 -3986.7743 756.24602 26987.371 -31731.456 304.46717 624.24229 1.0321373 0.002 -0.00048 0.00012
2095000 -3326.2775 602.99404 -3929.2715 749.8592 27051.296 -31732.523 279.40885 21.760593 0.97296422 0.002 -0.00048 0.00012
2100000 -3274.713 637.87108 -3912.5841 732.65727 27083.78 -31732.17 295.56979 240.14235 1.0031674 0.002 -0.00048 0.00012
Loop time of 725.602 on 12 procs for 100000 steps with 1085 atoms
Performance: 11.907 ns/day, 2.016 hours/ns, 137.817 timesteps/s
97.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 462 | 493.8 | 523.25 | 84.9 | 68.05
Bond | 0.1041 | 0.11809 | 0.14113 | 2.9 | 0.02
Kspace | 114.69 | 143.72 | 174.97 | 155.9 | 19.81
Neigh | 10.303 | 10.323 | 10.344 | 0.4 | 1.42
Comm | 28.859 | 32.028 | 33.623 | 28.9 | 4.41
Output | 0.004334 | 0.0043786 | 0.004731 | 0.2 | 0.00
Modify | 31.512 | 35.46 | 43.609 | 76.4 | 4.89
Other | | 10.15 | | | 1.40
Nlocal: 90.4167 ave 100 max 74 min
Histogram: 1 0 1 0 1 2 0 3 2 2
Nghost: 3965.08 ave 4046 max 3914 min
Histogram: 2 1 1 2 4 0 0 1 0 1
Neighs: 0.833333 ave 10 max 0 min
Histogram: 11 0 0 0 0 0 0 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 4040
Dangerous builds = 0
# write_restart restart.*.lmp
write_data data.*.lmp
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28614108
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.01431379
estimated relative force accuracy = 4.3105553e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Total wall time: 4:23:20

2734
examples/USER/fep/CH4hyd/fdti10/log.lammps
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File diff suppressed because it is too large Load Diff

22
examples/USER/fep/CH4hyd/fep01/fep01.fep Normal file
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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.0924139 9400.63 10924.6
200000 0.24007 7502.01 10933.6
300000 0.444164 5573.73 10941
400000 0.72462 3736.66 10967.3
500000 0.750033 4691.89 10954.7
600000 0.642574 5400.68 10991.8
700000 0.43362 7126.12 10974.7
800000 0.339885 7618.73 10966.1
900000 0.16755 9358.12 10977.1
1000000 0.0774989 10563.7 11016.4
1100000 0.0678746 10493.2 10967.1
1200000 -0.00129942 11479.7 10995.5
1300000 -0.0193415 11762.7 10996.7
1400000 -0.0271895 11872.4 10995.1
1500000 -0.0533096 12288.7 10985.2
1600000 -0.0785828 12759.6 10999.8
1700000 -0.0930725 13034 11026.1
1800000 -0.115192 13431.8 10994.5
1900000 -0.138539 13934.9 10998.2
2000000 -0.162228 14431.7 10965

22
examples/USER/fep/CH4hyd/fep01/fep01.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.0735182 0.889583
200000 0.241868 0.679931
300000 0.407677 0.542008
400000 0.709112 0.360902
500000 0.718538 0.428553
600000 0.639674 0.516854
700000 0.482835 0.586307
800000 0.289216 0.746055
900000 0.192641 0.823932
1000000 0.113029 0.908737
1100000 0.0619301 0.96572
1200000 0.0197356 1.01976
1300000 0.00310596 1.03223
1400000 -0.0300484 1.08295
1500000 -0.0714914 1.14599
1600000 -0.0712604 1.14573
1700000 -0.109089 1.2123
1800000 -0.117256 1.22671
1900000 -0.132337 1.25534
2000000 -0.153557 1.29745

12
examples/USER/fep/CH4hyd/fep01/in.fep01.lmp
View File

@ -41,7 +41,7 @@ timestep 1.0
velocity all create ${TK} 12345
thermo_style multi
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
@ -49,6 +49,7 @@ fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
set type 1*2 charge 0.0
run 100000
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
@ -61,7 +62,7 @@ fix ADAPT all adapt/fep 100000 &
atom charge 2 v_q2 &
after yes
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal 0.05
variable dq1 equal -0.24*v_dlambda
@ -70,11 +71,12 @@ variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} &
pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2
atom charge 2 v_dq2 &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep01.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000

702
examples/USER/fep/CH4hyd/fep01/log.fep01 Normal file
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@ -0,0 +1,702 @@
LAMMPS (29 Oct 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# created by fftool
print "Methane in TIP4P water"
Methane in TIP4P water
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.lmp
Reading data file ...
orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
2 by 2 by 3 MPI processor grid
reading atoms ...
1085 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
724 bonds
reading angles ...
366 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.015 seconds
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm/tip4p 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
pair_coeff 1 3 lj/cut/tip4p/long/soft 0.1036 3.3279 0.0 # C4H Ow
pair_coeff 1 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # C4H Hw
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
variable TK equal 300.0
variable PBAR equal 1.0
fix SHAKE all shake 0.0001 20 0 b 2 a 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
360 = # of frozen angles
find clusters CPU = 0.001 seconds
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
velocity all create 300 12345
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 1 1000
set type 1*2 charge 0.0
Setting atom values ...
5 settings made for charge
run 100000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.27021504
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.025869595
estimated relative force accuracy = 7.7905518e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.87 | 10.88 | 10.90 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density
0 548.49163 647.43194 -98.940309 -203.16773 29916.943 -29812.884 300 792.60653 0.55642578
5000 -3289.6503 661.8139 -3951.4642 745.98638 25311.37 -30009.296 306.66415 59.150479 0.99224242
10000 -3264.0347 685.09114 -3949.1258 773.73595 25289.123 -30012.539 317.45011 777.39342 0.98636787
15000 -3251.5551 648.11398 -3899.6691 671.398 25441.786 -30013.334 300.31603 -413.14206 1.016661
20000 -3252.4 689.36359 -3941.7636 737.7343 25333.597 -30013.526 319.42983 -21.174789 0.97535351
25000 -3338.3947 615.37903 -3953.7737 787.76879 25271.858 -30013.71 285.14767 1017.286 0.99756551
30000 -3284.3985 677.49887 -3961.8974 762.04248 25284.899 -30009.413 313.93209 244.39314 0.97967112
35000 -3261.5411 666.45457 -3927.9957 733.96743 25351.027 -30013.599 308.8145 -110.12637 0.96937976
40000 -3234.8532 623.53317 -3858.3863 713.89789 25437.451 -30010.345 288.92605 8.4228945 0.97303537
45000 -3355.6584 635.78023 -3991.4386 847.07484 25173.275 -30012.205 294.60096 1998.0377 1.0016853
50000 -3289.0168 631.74466 -3920.7614 746.01676 25347.251 -30014.586 292.731 72.499979 0.98411892
55000 -3317.0357 623.56712 -3940.6028 761.336 25307.662 -30010.219 288.94178 631.58596 0.99041384
60000 -3235.6514 670.35907 -3906.0105 763.2789 25342.581 -30012.557 310.62372 485.74187 0.96692138
65000 -3289.6272 631.91655 -3921.5438 726.6807 25361.327 -30009.98 292.81065 -39.822331 0.98670912
70000 -3356.7387 634.65207 -3991.3908 759.18886 25260.804 -30011.846 294.0782 -279.67723 0.96104105
75000 -3339.1035 646.63311 -3985.7366 740.57966 25283.92 -30010.741 299.62985 -663.63274 0.97015795
80000 -3315.2349 629.58698 -3944.8219 703.81392 25361.66 -30010.869 291.7312 -274.07447 1.0083118
85000 -3287.7679 646.81739 -3934.5853 715.97889 25360.677 -30011.833 299.71524 -446.21411 0.99175345
90000 -3328.6167 643.38471 -3972.0014 799.56485 25239.915 -30011.926 298.12464 1554.6031 1.0204346
95000 -3309.6011 644.25764 -3953.8587 772.13317 25285.772 -30012.282 298.52913 714.97326 0.99859772
100000 -3234.6909 663.02311 -3897.714 742.089 25372.74 -30012.966 307.22446 626.49142 0.98804377
Loop time of 668.747 on 12 procs for 100000 steps with 1085 atoms
Performance: 12.920 ns/day, 1.858 hours/ns, 149.533 timesteps/s
96.8% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 406.74 | 439.26 | 465.65 | 70.5 | 65.68
Bond | 0.087756 | 0.10996 | 0.13947 | 5.4 | 0.02
Kspace | 118.68 | 145.09 | 177.35 | 122.1 | 21.70
Neigh | 10.16 | 10.19 | 10.211 | 0.5 | 1.52
Comm | 27.812 | 30.7 | 32.07 | 27.5 | 4.59
Output | 0.0012463 | 0.0012851 | 0.0016544 | 0.3 | 0.00
Modify | 31.302 | 34.865 | 42.23 | 71.4 | 5.21
Other | | 8.521 | | | 1.27
Nlocal: 90.4167 ave 99 max 79 min
Histogram: 1 1 0 0 2 2 1 1 3 1
Nghost: 3895.83 ave 3960 max 3844 min
Histogram: 2 3 0 1 0 1 1 2 1 1
Neighs: 0.833333 ave 6 max 0 min
Histogram: 10 0 0 0 0 0 1 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 4076
Dangerous builds = 1
reset_timestep 0
variable lambda equal ramp(0.0,1.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix ADAPT all adapt/fep 100000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda atom charge 1 v_q1 atom charge 2 v_q2 after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal 0.05
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
compute FEP all fep 300 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep01.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28574247
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014533761
estimated relative force accuracy = 4.3767988e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
FEP settings ...
temperature = 300.000000
tail no
lj/cut/tip4p/long/soft lambda 1-2 3-4
1-1 charge
2-2 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.17 | 12.18 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_q1 v_q2
0 -3234.7709 663.02311 -3897.794 742.089 27095.239 -31735.545 307.22446 699.17165 0.98804377 0 -0 0
5000 -3289.0224 631.33682 -3920.3592 731.99995 27081.876 -31734.814 292.54202 -179.44137 0.99284002 0.0025 -0.0006 0.00015
10000 -3299.1847 676.16148 -3975.3462 708.59345 27050.107 -31734.496 313.31238 -518.83651 0.99067088 0.005 -0.0012 0.0003
15000 -3302.2326 642.06473 -3944.2973 725.78424 27062.847 -31733.405 297.513 -508.19421 0.98063265 0.0075 -0.0018 0.00045
20000 -3296.4091 644.34799 -3940.7571 742.59645 27053.208 -31737.038 298.57099 116.68509 0.99271503 0.01 -0.0024 0.0006
25000 -3329.7456 639.23547 -3968.9811 783.76339 26982.097 -31735.383 296.20201 496.16152 0.97684075 0.0125 -0.003 0.00075
30000 -3290.8879 622.28019 -3913.1681 761.24177 27062.793 -31737.656 288.34545 1324.9373 1.020133 0.015 -0.0036 0.0009
35000 -3258.8976 654.70358 -3913.6012 720.26437 27101.834 -31736.017 303.36945 -12.98411 0.98568197 0.0175 -0.0042 0.00105
40000 -3316.6813 661.50653 -3978.1879 744.40073 27012.054 -31735.136 306.52173 -328.49176 0.98122496 0.02 -0.0048 0.0012
45000 -3328.8398 626.57382 -3955.4137 767.73554 27012.692 -31736.292 290.33499 216.96405 0.98739876 0.0225 -0.0054 0.00135
50000 -3340.9891 657.35839 -3998.3475 830.88061 26901.969 -31731.639 304.59961 1277.8313 0.9894139 0.025 -0.006 0.0015
55000 -3286.6334 664.03418 -3950.6675 693.37215 27091.208 -31735.635 307.69297 -1169.7207 0.97446921 0.0275 -0.0066 0.00165
60000 -3284.1129 649.62828 -3933.7411 742.27197 27058.071 -31734.367 301.01772 217.61495 0.99138135 0.03 -0.0072 0.0018
65000 -3278.0768 656.07593 -3934.1527 802.64294 26995.676 -31733.004 304.00536 1438.6113 0.99167193 0.0325 -0.0078 0.00195
70000 -3257.071 646.97756 -3904.0486 784.2684 27041.692 -31730.549 299.78945 1105.7892 0.97904694 0.035 -0.0084 0.0021
75000 -3302.3867 616.53809 -3918.9247 724.15443 27092.319 -31735.774 285.68474 -257.61941 0.98545045 0.0375 -0.009 0.00225
80000 -3273.1943 666.82395 -3940.0182 710.93871 27084.085 -31735.513 308.98566 -793.05223 0.97840301 0.04 -0.0096 0.0024
85000 -3265.5621 673.58344 -3939.1455 718.18264 27076.343 -31734.09 312.1178 -266.75978 0.99570803 0.0425 -0.0102 0.00255
90000 -3290.206 653.64139 -3943.8474 639.00442 27149.273 -31732.703 302.87727 -2090.0779 0.98198222 0.045 -0.0108 0.0027
95000 -3331.8751 640.75522 -3972.6303 741.43112 27017.822 -31732.42 296.90621 -273.00408 0.98683047 0.0475 -0.0114 0.00285
100000 -3296.8724 646.00751 -3942.8799 692.35792 27098.667 -31734.399 299.33996 -1122.9346 0.96037747 0.05 -0.012 0.003
105000 -3323.043 660.68623 -3983.7293 725.81149 27024.038 -31733.834 306.14163 -478.30302 1.0026308 0.0525 -0.0126 0.00315
110000 -3293.647 644.60735 -3938.2544 773.7496 27021.39 -31733.875 298.69117 434.89378 0.96738408 0.055 -0.0132 0.0033
115000 -3318.6094 617.95787 -3936.5672 711.01122 27087.703 -31735.935 286.34262 -586.06437 0.9963844 0.0575 -0.0138 0.00345
120000 -3318.7136 619.55912 -3938.2728 711.36644 27085.947 -31736.008 287.08459 -174.13483 1.0014176 0.06 -0.0144 0.0036
125000 -3311.5169 619.86219 -3931.3791 740.06281 27062.525 -31734.232 287.22503 95.093205 0.98984372 0.0625 -0.015 0.00375
130000 -3257.5389 660.71935 -3918.2582 743.22185 27073.512 -31735.593 306.15698 691.41882 1.0024 0.065 -0.0156 0.0039
135000 -3234.1888 663.45494 -3897.6437 703.73158 27132.827 -31734.715 307.42456 -485.33417 0.96446007 0.0675 -0.0162 0.00405
140000 -3328.5262 611.78779 -3940.314 758.21124 27032.974 -31731.986 283.4836 291.77762 0.99457944 0.07 -0.0168 0.0042
145000 -3324.8731 622.90615 -3947.7792 753.6117 27033.123 -31735.186 288.6355 343.24728 1.0157261 0.0725 -0.0174 0.00435
150000 -3326.137 623.51882 -3949.6559 781.40757 27001.12 -31732.581 288.9194 379.64232 0.97830823 0.075 -0.018 0.0045
155000 -3267.7496 642.82809 -3910.5777 711.45054 27113.985 -31736.481 297.86672 -292.80529 0.99361431 0.0775 -0.0186 0.00465
160000 -3299.5989 662.74649 -3962.3454 712.8089 27056.164 -31731.87 307.09629 -496.04777 0.99183864 0.08 -0.0192 0.0048
165000 -3329.291 646.32489 -3975.6159 801.98506 26958.482 -31736.573 299.48702 997.42028 0.98284724 0.0825 -0.0198 0.00495
170000 -3318.536 653.82172 -3972.3577 786.6347 26975.18 -31734.52 302.96083 1334.3627 1.0236211 0.085 -0.0204 0.0051
175000 -3325.4627 619.69669 -3945.1594 690.02714 27098.09 -31733.687 287.14834 -919.83628 0.99453856 0.0875 -0.021 0.00525
180000 -3300.3031 636.65018 -3936.9533 745.64489 27054.483 -31737.57 295.00406 219.06021 0.99348984 0.09 -0.0216 0.0054
185000 -3203.2521 676.13783 -3879.3899 745.60713 27109.132 -31734.768 313.30143 414.18855 0.9633435 0.0925 -0.0222 0.00555
190000 -3277.3235 646.22256 -3923.546 751.99067 27057.559 -31733.602 299.43961 413.00249 0.98434955 0.095 -0.0228 0.0057
195000 -3346.2223 647.85098 -3994.0733 767.89014 26969.502 -31731.781 300.19417 -28.507593 0.96832487 0.0975 -0.0234 0.00585
200000 -3300.1935 646.69629 -3946.8898 701.64088 27083.477 -31732.446 299.65912 -707.03161 0.99055336 0.1 -0.024 0.006
205000 -3290.9787 648.02246 -3939.0011 640.17442 27153.624 -31733.433 300.27363 -1956.9384 0.98696639 0.1025 -0.0246 0.00615
210000 -3274.8996 636.56925 -3911.4689 749.14043 27072.195 -31733.439 294.96656 57.011756 0.97283184 0.105 -0.0252 0.0063
215000 -3258.8914 649.62228 -3908.5137 730.52403 27095.576 -31734.9 301.01494 332.42518 1.0045487 0.1075 -0.0258 0.00645
220000 -3281.2031 642.14025 -3923.3434 643.85812 27165.046 -31732.913 297.54799 -1558.401 0.99750231 0.11 -0.0264 0.0066
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1520000 -3343.4048 649.78959 -3993.1944 759.77827 26984.954 -31738.378 301.09246 52.485546 0.98446475 0.76 -0.1824 0.0456
1525000 -3322.9361 661.2557 -3984.1918 774.88353 26972.178 -31734.008 306.4055 455.56018 0.98985739 0.7625 -0.183 0.04575
1530000 -3262.4433 651.35492 -3913.7982 752.35829 27066.466 -31734.426 301.81778 707.01467 0.98679728 0.765 -0.1836 0.0459
1535000 -3273.5767 648.64605 -3922.2227 739.90634 27068.98 -31733.955 300.56258 384.46783 0.99043836 0.7675 -0.1842 0.04605
1540000 -3265.5991 663.04868 -3928.6478 693.11761 27111.89 -31735.992 307.23632 -987.43418 0.97511395 0.77 -0.1848 0.0462
1545000 -3390.8206 627.3039 -4018.1245 774.86095 26939.969 -31734.684 290.67329 28.564843 0.98612112 0.7725 -0.1854 0.04635
1550000 -3290.8539 644.06407 -3934.9179 794.35106 27004.534 -31736.511 298.43943 1138.5426 0.97923789 0.775 -0.186 0.0465
1555000 -3314.6235 656.30394 -3970.9274 725.95449 27031.063 -31734.26 304.11101 -522.74463 0.98757231 0.7775 -0.1866 0.04665
1560000 -3348.4727 647.37982 -3995.8526 752.01885 26985.413 -31737.772 299.97585 -675.57461 0.96085139 0.78 -0.1872 0.0468
1565000 -3368.2949 667.06116 -4035.3561 790.24768 26909.901 -31739.61 309.09557 272.03468 0.98329116 0.7825 -0.1878 0.04695
1570000 -3294.9644 661.19425 -3956.1586 719.06049 27055.663 -31735.074 306.37703 -407.15013 0.97391759 0.785 -0.1884 0.0471
1575000 -3290.259 672.35805 -3962.6171 784.16731 26981.845 -31735.498 311.54999 411.32973 0.98026598 0.7875 -0.189 0.04725
1580000 -3320.2653 648.6179 -3968.8832 751.83606 27014.567 -31738.316 300.54954 112.93867 0.98106335 0.79 -0.1896 0.0474
1585000 -3348.3799 623.4693 -3971.8492 780.89962 26978.683 -31736.336 288.89645 198.22597 0.97410432 0.7925 -0.1902 0.04755
1590000 -3274.0179 664.97781 -3938.9957 743.12264 27049.949 -31734.725 308.13022 -149.0667 0.9665298 0.795 -0.1908 0.0477
1595000 -3223.9489 628.3249 -3852.2738 699.62234 27181.274 -31736.807 291.14638 -205.53009 0.96460847 0.7975 -0.1914 0.04785
1600000 -3301.6514 643.69587 -3945.3473 768.5055 27023.232 -31739.965 298.26882 803.28885 0.9902691 0.8 -0.192 0.048
1605000 -3330.516 649.38916 -3979.9051 770.36543 26984.062 -31736.765 300.90692 286.896 0.9890256 0.8025 -0.1926 0.04815
1610000 -3290.1032 665.01988 -3955.1231 736.02699 27046.172 -31738.477 308.14971 33.796683 0.98154372 0.805 -0.1932 0.0483
1615000 -3293.4066 645.09892 -3938.5055 748.81674 27043.129 -31734.875 298.91895 179.08584 0.97559262 0.8075 -0.1938 0.04845
1620000 -3286.6996 699.9527 -3986.6523 755.18177 26990.669 -31735.947 324.3365 -424.78507 0.96328116 0.81 -0.1944 0.0486
1625000 -3359.4441 625.7752 -3985.2193 762.89599 26986.401 -31737.759 289.96493 -106.50856 0.97608975 0.8125 -0.195 0.04875
1630000 -3356.4827 620.3765 -3976.8592 752.04319 27008.833 -31739.838 287.46334 68.079862 0.9851356 0.815 -0.1956 0.0489
1635000 -3311.9095 625.18537 -3937.0948 740.08264 27052.358 -31735.068 289.69162 195.45285 0.98578062 0.8175 -0.1962 0.04905
1640000 -3282.2577 633.58191 -3915.8396 706.57523 27107.6 -31733.057 293.58232 -559.59294 0.97877977 0.82 -0.1968 0.0492
1645000 -3282.711 656.7138 -3939.4248 741.57401 27053.58 -31736.179 304.30093 -59.692487 0.97422366 0.8225 -0.1974 0.04935
1650000 -3310.8621 642.03596 -3952.898 762.28147 27017.909 -31734.631 297.49967 671.6923 0.99038515 0.825 -0.198 0.0495
1655000 -3263.6876 670.83498 -3934.5226 702.31573 27098.073 -31738.575 310.84425 -946.7917 0.97916207 0.8275 -0.1986 0.04965
1660000 -3285.1857 678.41086 -3963.5966 757.92725 27011.819 -31735.683 314.35468 384.23549 0.98644252 0.83 -0.1992 0.0498
1665000 -3252.9457 694.14474 -3947.0905 712.30879 27076.129 -31737.086 321.64527 -646.87417 0.96762975 0.8325 -0.1998 0.04995
1670000 -3305.871 619.27179 -3925.1428 737.61963 27073.074 -31737.532 286.95145 60.456806 0.98147319 0.835 -0.2004 0.0501
1675000 -3319.7118 643.14189 -3962.8537 733.15066 27034.087 -31733.898 298.01212 -335.68221 0.97040794 0.8375 -0.201 0.05025
1680000 -3282.2367 648.60366 -3930.8403 697.80758 27106.979 -31737.678 300.54294 -821.93638 0.97624892 0.84 -0.2016 0.0504
1685000 -3349.7097 610.17553 -3959.8852 714.2204 27061.577 -31739.049 282.73653 -608.03338 0.97715725 0.8425 -0.2022 0.05055
1690000 -3276.8907 654.19286 -3931.0836 753.31199 27051.143 -31737.814 303.1328 470.52169 1.0040827 0.845 -0.2028 0.0507
1695000 -3356.5028 624.6713 -3981.1741 721.8757 27033.813 -31738.204 289.45342 -594.09001 0.98851274 0.8475 -0.2034 0.05085
1700000 -3323.8154 626.79844 -3950.6138 744.24997 27041.346 -31738.556 290.43907 24.956241 0.98825494 0.85 -0.204 0.051
1705000 -3242.9786 679.9754 -3922.954 654.28813 27159.104 -31738.27 315.07963 -1251.9879 0.99005714 0.8525 -0.2046 0.05115
1710000 -3311.427 658.82294 -3970.25 721.93221 27043.021 -31738.466 305.27824 -621.60252 0.99919856 0.855 -0.2052 0.0513
1715000 -3321.1662 654.12092 -3975.2871 748.1525 27013.147 -31738.133 303.09946 199.42662 0.98584932 0.8575 -0.2058 0.05145
1720000 -3252.9739 630.37518 -3883.3491 764.34959 27086.819 -31735.934 292.09642 590.47908 0.96914932 0.86 -0.2064 0.0516
1725000 -3355.7913 629.38324 -3985.1745 773.89334 26977.905 -31738.013 291.63679 424.70863 0.98894849 0.8625 -0.207 0.05175
1730000 -3265.7677 679.33001 -3945.0977 741.70993 27044.967 -31735.714 314.78058 -156.32001 0.96682119 0.865 -0.2076 0.0519
1735000 -3329.3178 631.04003 -3960.3579 728.61842 27044.399 -31735.951 292.40449 -617.28914 0.9779626 0.8675 -0.2082 0.05205
1740000 -3276.4172 652.18346 -3928.6006 711.76567 27095.339 -31737.13 302.20171 -608.64098 0.97577767 0.87 -0.2088 0.0522
1745000 -3367.0629 619.23699 -3986.2999 714.70504 27034.572 -31738.184 286.93533 -881.7967 0.98850571 0.8725 -0.2094 0.05235
1750000 -3350.0569 625.65732 -3975.7142 730.88885 27025.633 -31734.804 289.91031 -297.14279 0.9893824 0.875 -0.21 0.0525
1755000 -3338.301 633.65415 -3971.9552 775.28876 26985.334 -31736.591 293.61579 412.3181 0.98557765 0.8775 -0.2106 0.05265
1760000 -3251.9064 667.70039 -3919.6068 795.48855 27019.487 -31738.029 309.39177 1649.3602 0.99301618 0.88 -0.2112 0.0528
1765000 -3297.0745 627.67022 -3924.7447 770.52235 27039.901 -31737.82 290.84303 857.08221 1.0083534 0.8825 -0.2118 0.05295
1770000 -3271.0779 654.10045 -3925.1783 728.58424 27081.992 -31739.013 303.08998 -88.428469 0.98111355 0.885 -0.2124 0.0531
1775000 -3346.407 605.46892 -3951.8759 742.13304 27039.004 -31735.678 280.55563 343.16771 0.99968234 0.8875 -0.213 0.05325
1780000 -3290.5326 661.67685 -3952.2094 760.33686 27023.324 -31738.767 306.60065 402.19944 0.99400686 0.89 -0.2136 0.0534
1785000 -3366.1206 638.40054 -4004.5211 751.36335 26975.592 -31735.746 295.81513 -269.13878 0.97165913 0.8925 -0.2142 0.05355
1790000 -3258.3055 622.65513 -3880.9606 676.40276 27176.903 -31736.935 288.51919 -830.57704 0.98709996 0.895 -0.2148 0.0537
1795000 -3312.0411 642.61352 -3954.6546 750.65851 27027.881 -31736.946 297.76729 340.63468 0.99666772 0.8975 -0.2154 0.05385
1800000 -3340.1029 629.50175 -3969.6047 755.54335 27008.136 -31736.646 291.6917 -362.32152 0.97026562 0.9 -0.216 0.054
1805000 -3239.5085 671.40118 -3910.9097 721.78691 27097.089 -31733.431 311.1066 110.04563 0.96382704 0.9025 -0.2166 0.05415
1810000 -3266.7865 684.65149 -3951.4379 757.10372 27027.29 -31737.399 317.24639 729.96782 1.0049447 0.905 -0.2172 0.0543
1815000 -3333.81 654.59809 -3988.4081 796.79491 26953.479 -31739.86 303.32057 730.60501 0.97490606 0.9075 -0.2178 0.05445
1820000 -3340.6271 615.49021 -3956.1173 771.71374 27012.552 -31741.723 285.19919 565.28134 0.98472964 0.91 -0.2184 0.0546
1825000 -3298.7504 643.65917 -3942.4095 724.49708 27069.231 -31738.213 298.25181 -298.62774 0.96726328 0.9125 -0.219 0.05475
1830000 -3290.9971 666.44583 -3957.443 668.19041 27111.858 -31739.915 308.81045 -1725.0885 0.97076205 0.915 -0.2196 0.0549
1835000 -3254.7179 677.57424 -3932.2922 726.00793 27078.89 -31740.472 313.96701 -300.48129 0.97472843 0.9175 -0.2202 0.05505
1840000 -3259.1244 703.38585 -3962.5102 754.37475 27017.218 -31737.576 325.92731 396.08403 0.99224318 0.92 -0.2208 0.0552
1845000 -3262.1107 624.81539 -3886.9261 719.208 27127.288 -31736.726 289.52019 205.96515 0.98538694 0.9225 -0.2214 0.05535
1850000 -3341.4941 642.35109 -3983.8452 753.00292 27001.459 -31740.126 297.64569 -115.99892 0.97327886 0.925 -0.222 0.0555
1855000 -3319.9831 602.04025 -3922.0234 742.3858 27073.567 -31741.193 278.96689 -7.4449495 0.98220359 0.9275 -0.2226 0.05565
1860000 -3306.9705 679.97559 -3986.9461 826.7132 26917.659 -31735.844 315.07972 995.54048 0.97137783 0.93 -0.2232 0.0558
1865000 -3293.9564 665.98336 -3959.9398 748.22311 27023.987 -31737.053 308.59616 726.98864 1.0142172 0.9325 -0.2238 0.05595
1870000 -3237.963 655.69966 -3893.6627 726.58511 27111.384 -31737.594 303.831 -21.727181 0.97281044 0.935 -0.2244 0.0561
1875000 -3374.6595 619.66759 -3994.3271 726.44658 27013.079 -31737.214 287.13485 -276.33824 1.0045608 0.9375 -0.225 0.05625
1880000 -3277.6826 660.5116 -3938.1942 744.90816 27048.289 -31732.964 306.06071 208.07192 0.98192071 0.94 -0.2256 0.0564
1885000 -3303.7764 641.96127 -3945.7377 700.82697 27086.5 -31737.254 297.46506 -705.0392 0.99500598 0.9425 -0.2262 0.05655
1890000 -3359.8447 609.89199 -3969.7367 700.20487 27066.841 -31738.549 282.60514 -713.02909 1.000895 0.945 -0.2268 0.0567
1895000 -3312.62 622.92578 -3935.5457 770.82145 27029.24 -31739.059 288.6446 1173.4526 1.0063156 0.9475 -0.2274 0.05685
1900000 -3308.4458 669.47072 -3977.9165 760.07479 26994.212 -31736.251 310.21209 -36.382368 0.97889335 0.95 -0.228 0.057
1905000 -3370.217 651.08853 -4021.3056 729.87681 26986.245 -31740.306 301.69435 -892.25427 0.98214988 0.9525 -0.2286 0.05715
1910000 -3297.6045 614.14852 -3911.753 725.77044 27099.174 -31739.96 284.57749 -123.36078 0.97752647 0.955 -0.2292 0.0573
1915000 -3292.1458 626.31854 -3918.4644 710.0067 27105.45 -31738.665 290.2167 -156.06234 0.98706768 0.9575 -0.2298 0.05745
1920000 -3258.6317 683.05625 -3941.688 733.15963 27058.48 -31737.899 316.50721 -331.27328 0.96792 0.96 -0.2304 0.0576
1925000 -3308.3003 643.25078 -3951.5511 734.71807 27042.131 -31733.678 298.06258 -899.10835 0.95191489 0.9625 -0.231 0.05775
1930000 -3275.685 662.2037 -3937.8887 716.74146 27078.527 -31736.562 306.84478 -54.012541 1.0043314 0.965 -0.2316 0.0579
1935000 -3287.9716 633.56371 -3921.5353 746.44129 27064.22 -31736.176 293.57389 1037.5548 1.0147673 0.9675 -0.2322 0.05805
1940000 -3250.1051 685.34381 -3935.4489 774.55817 27023.81 -31739.014 317.56719 1418.383 1.0125818 0.97 -0.2328 0.0582
1945000 -3270.0763 642.65027 -3912.7266 697.73057 27121.723 -31738.163 297.78432 -479.20715 0.98729311 0.9725 -0.2334 0.05835
1950000 -3334.5536 631.76366 -3966.3173 699.41626 27068.476 -31736.481 292.7398 -957.14355 0.97960776 0.975 -0.234 0.0585
1955000 -3276.8103 652.29988 -3929.1102 737.65435 27070.22 -31738.521 302.25565 262.50358 1.0038568 0.9775 -0.2346 0.05865
1960000 -3332.6922 636.66505 -3969.3573 705.90837 27055.869 -31736.072 295.01095 -833.658 0.97874229 0.98 -0.2352 0.0588
1965000 -3341.1449 667.15503 -4008.2999 810.06486 26919.746 -31741.042 309.13907 1144.3005 0.99581793 0.9825 -0.2358 0.05895
1970000 -3271.8283 655.42621 -3927.2545 789.31365 27019.023 -31737.916 303.7043 1151.1363 0.99225241 0.985 -0.2364 0.0591
1975000 -3300.0112 644.65396 -3944.6652 745.21042 27048.054 -31739.819 298.71277 136.49822 0.97832039 0.9875 -0.237 0.05925
1980000 -3335.2376 663.40445 -3998.642 758.8957 26979.416 -31739.34 307.40117 58.763635 0.9885575 0.99 -0.2376 0.0594
1985000 -3325.927 630.5991 -3956.5261 756.54904 27023.943 -31738.779 292.20018 85.287803 0.98050884 0.9925 -0.2382 0.05955
1990000 -3321.7443 646.44654 -3968.1909 721.63898 27049.911 -31741.98 299.54339 -748.66083 0.97438047 0.995 -0.2388 0.0597
1995000 -3330.3216 635.32254 -3965.6441 757.24268 27013.893 -31738.755 294.38888 174.06377 0.99429928 0.9975 -0.2394 0.05985
2000000 -3288.8004 648.87481 -3937.6752 759.37954 27037.886 -31738.632 300.66858 576.95398 0.9825578 1 -0.24 0.06
Loop time of 14303.5 on 12 procs for 2000000 steps with 1085 atoms
Performance: 12.081 ns/day, 1.987 hours/ns, 139.826 timesteps/s
97.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8597.9 | 9509.6 | 10454 | 480.9 | 66.48
Bond | 1.7877 | 2.2559 | 2.8669 | 19.7 | 0.02
Kspace | 2141.2 | 3082 | 3987.1 | 842.0 | 21.55
Neigh | 203.37 | 203.86 | 204.5 | 2.2 | 1.43
Comm | 563.03 | 621.88 | 649.79 | 120.5 | 4.35
Output | 0.087605 | 0.088635 | 0.095602 | 0.7 | 0.00
Modify | 621.62 | 690.96 | 836.21 | 314.9 | 4.83
Other | | 192.8 | | | 1.35
Nlocal: 90.4167 ave 96 max 82 min
Histogram: 1 0 1 1 1 1 2 2 1 2
Nghost: 3917.17 ave 3994 max 3861 min
Histogram: 3 0 3 0 1 1 1 2 0 1
Neighs: 0.833333 ave 4 max 0 min
Histogram: 8 0 1 0 0 1 0 1 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 80894
Dangerous builds = 0
# write_restart restart.*.lmp
write_data data.*.lmp
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.2855962
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014616839
estimated relative force accuracy = 4.4018178e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Total wall time: 4:09:32

2736
examples/USER/fep/CH4hyd/fep01/log.lammps
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22
examples/USER/fep/CH4hyd/fep10/fep10.fep Normal file
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@ -0,0 +1,22 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2] c_FEP[3]
100000 0.158157 8461.17 11000.7
200000 0.139178 8759.55 11001
300000 0.128455 8934.01 11008.5
400000 0.116877 9111.62 10984.6
500000 0.0959445 9536.39 11034.6
600000 0.0799249 9773.35 10979.5
700000 0.0720308 9995.68 11018.3
800000 0.0517984 10422 11007.4
900000 0.047168 10511.6 10986.7
1000000 -0.0106684 11744.2 10959
1100000 -0.0333101 12445.3 10955.3
1200000 0.000259362 11553.2 10975.3
1300000 -0.0989019 15082.8 11002.9
1400000 -0.136202 16006.9 11015.9
1500000 -0.35317 28280.3 10979.5
1600000 -0.376527 27994.4 10941.1
1700000 -0.466717 28704.9 10977.5
1800000 -0.40276 22879.4 10952.8
1900000 -0.236423 16600.5 10966
2000000 -0.0676637 12337.9 10936.9

22
examples/USER/fep/CH4hyd/fep10/fep10.lmp
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@ -1,22 +0,0 @@
# Time-averaged data for fix FEP
# TimeStep c_FEP[1] c_FEP[2]
100000 0.160455 0.766272
200000 0.141912 0.791902
300000 0.119585 0.824744
400000 0.104694 0.847809
500000 0.0917124 0.869318
600000 0.0859541 0.881974
700000 0.0666319 0.920268
800000 0.0428654 0.965893
900000 0.0240106 0.999889
1000000 0.0294147 0.997671
1100000 -0.0214947 1.11583
1200000 -0.0543642 1.23078
1300000 -0.0665772 1.25986
1400000 -0.196675 1.66521
1500000 -0.341037 2.39926
1600000 -0.480217 2.97287
1700000 -0.405599 2.36311
1800000 -0.415165 2.12414
1900000 -0.229669 1.49644
2000000 -0.0838847 1.15743

11
examples/USER/fep/CH4hyd/fep10/in.fep10.lmp
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@ -41,7 +41,7 @@ timestep 1.0
velocity all create ${TK} 12345
thermo_style multi
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
@ -60,7 +60,7 @@ fix ADAPT all adapt/fep 100000 &
atom charge 2 v_q2 &
after yes
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal -0.05
variable dq1 equal -0.24*v_dlambda
@ -69,11 +69,12 @@ variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} &
pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
atom charge 1 v_dq1 &
atom charge 2 v_dq2
atom charge 2 v_dq2 &
volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep10.lmp
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000

698
examples/USER/fep/CH4hyd/fep10/log.fep10 Normal file
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@ -0,0 +1,698 @@
LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/lammps/src/comm.cpp:94)
using 1 OpenMP thread(s) per MPI task
# created by fftool
print "Methane in TIP4P water"
Methane in TIP4P water
units real
boundary p p p
atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5
read_data data.lmp
Reading data file ...
orthogonal box = (-13.443762 -13.443762 -13.443762) to (13.443762 13.443762 13.443762)
2 by 2 by 3 MPI processor grid
reading atoms ...
1085 atoms
scanning bonds ...
1 = max bonds/atom
scanning angles ...
6 = max angles/atom
reading bonds ...
724 bonds
reading angles ...
366 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0.5
special bond factors coul: 0 0 0.5
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
3 = max # of 1-4 neighbors
4 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
pair_style hybrid lj/cut/coul/long 10.0 10.0 lj/cut/tip4p/long/soft 3 4 2 2 0.125 1 0.5 10.0 10.0 10.0
pair_modify tail no
kspace_style pppm/tip4p 1.0e-4
pair_coeff 1 1 lj/cut/coul/long 0.0660 3.5000 # C4H C4H
pair_coeff 1 2 lj/cut/coul/long 0.0445 2.9580 # C4H H
pair_coeff 2 2 lj/cut/coul/long 0.0300 2.5000 # H H
pair_coeff 3 3 lj/cut/tip4p/long/soft 0.1628 3.1644 1.0 # Ow Ow
pair_coeff 3 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Ow Hw
pair_coeff 4 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # Hw Hw
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
variable TK equal 300.0
variable PBAR equal 1.0
fix SHAKE all shake 0.0001 20 0 b 2 a 2
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
360 = # of frozen angles
find clusters CPU = 0.001 seconds
neighbor 2.0 bin
timestep 1.0
velocity all create ${TK} 12345
velocity all create 300 12345
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density
thermo 5000
fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso ${PBAR} ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 ${PBAR} 1000
fix TPSTAT all npt temp 300 300 100 iso 1 1 1000
run 100000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.27021504
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.025872736
estimated relative force accuracy = 7.7914976e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 5 5 5
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.87 | 10.88 | 10.90 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density
0 546.33019 647.43194 -101.10176 -205.36298 29920.627 -29816.534 300 788.91776 0.55642578
5000 -3293.7887 627.99038 -3921.7791 719.6947 25372.789 -30015.189 290.99138 -479.95734 0.9593797
10000 -3331.8077 662.98464 -3994.7923 713.75931 25307.342 -30018.317 307.20664 -898.12579 0.98999504
15000 -3301.0664 627.03645 -3928.1029 713.74138 25370.946 -30014.046 290.54936 -109.9857 0.99219341
20000 -3297.0753 653.68091 -3950.7562 690.09393 25371.803 -30016.409 302.89558 -1292.1349 0.97162179
25000 -3275.1265 686.51678 -3961.6433 721.21849 25332.103 -30016.791 318.11071 -782.2511 0.96262585
30000 -3319.4764 641.48819 -3960.9646 695.13846 25358.256 -30016.462 297.24585 -1032.3693 0.97723105
35000 -3339.5958 640.96354 -3980.5593 746.14675 25286.621 -30016.405 297.00274 -144.41371 0.99597619
40000 -3303.8432 650.4284 -3954.2716 763.59884 25292.808 -30013.426 301.38846 290.54097 0.97091267
45000 -3288.6614 644.14778 -3932.8092 738.75427 25339.802 -30013.275 298.47822 203.13743 0.98353192
50000 -3314.5145 647.31284 -3961.8273 734.66685 25319.659 -30017.097 299.94481 -575.98875 0.96495858
55000 -3325.2116 627.09779 -3952.3094 758.50764 25300.029 -30012.977 290.57778 115.22411 0.96610359
60000 -3279.2821 660.91919 -3940.2013 777.80296 25297.967 -30017.7 306.24957 512.56809 0.95818026
65000 -3348.4144 627.03753 -3975.4519 663.13879 25377.083 -30017.103 290.54986 -1659.0852 0.99578827
70000 -3217.4766 677.26277 -3894.7394 720.54024 25395.021 -30012.777 313.82269 375.82022 0.99971463
75000 -3281.149 677.15421 -3958.3032 733.96553 25322.666 -30016.859 313.77238 -255.76801 0.98119917
80000 -3305.1444 657.51092 -3962.6553 791.41752 25259.267 -30014.718 304.67029 1173.0658 0.99379829
85000 -3304.8727 630.4153 -3935.288 735.79644 25341.978 -30016.371 292.11501 -267.42267 0.96149675
90000 -3300.5216 656.36473 -3956.8864 760.14613 25296.025 -30017.438 304.13918 414.5575 0.98279507
95000 -3278.8725 650.70078 -3929.5733 716.16787 25367.048 -30014.72 301.51468 -390.98983 0.97417615
100000 -3294.7866 648.37071 -3943.1573 689.04498 25379.449 -30013.819 300.435 -1095.9528 0.98149922
Loop time of 669.917 on 12 procs for 100000 steps with 1085 atoms
Performance: 12.897 ns/day, 1.861 hours/ns, 149.272 timesteps/s
96.8% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 402.61 | 445.28 | 475.76 | 108.3 | 66.47
Bond | 0.07811 | 0.11159 | 0.23902 | 14.3 | 0.02
Kspace | 109 | 139.2 | 182.04 | 193.5 | 20.78
Neigh | 10.026 | 10.046 | 10.071 | 0.5 | 1.50
Comm | 27.701 | 30.984 | 32.284 | 31.8 | 4.63
Output | 0.0012085 | 0.0012518 | 0.0016687 | 0.4 | 0.00
Modify | 30.502 | 34.847 | 43.475 | 84.1 | 5.20
Other | | 9.442 | | | 1.41
Nlocal: 90.4167 ave 100 max 78 min
Histogram: 1 0 0 3 1 2 0 1 2 2
Nghost: 3899.33 ave 3973 max 3848 min
Histogram: 2 1 2 2 1 0 2 0 0 2
Neighs: 0.833333 ave 10 max 0 min
Histogram: 11 0 0 0 0 0 0 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 4057
Dangerous builds = 1
reset_timestep 0
variable lambda equal ramp(1.0,0.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix ADAPT all adapt/fep 100000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda atom charge 1 v_q1 atom charge 2 v_q2 after yes
thermo_style custom step etotal ke pe evdwl ecoul elong temp press density v_lambda v_q1 v_q2
variable dlambda equal -0.05
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute FEP all fep ${TK} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
compute FEP all fep 300 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda atom charge 1 v_dq1 atom charge 2 v_dq2 volume yes
fix FEP all ave/time 20 4000 100000 c_FEP[*] file fep10.fep
dump TRAJ all custom 20000 dump.lammpstrj id mol type element xu yu zu
dump_modify TRAJ element C H O H
run 2000000
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28556787
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014632842
estimated relative force accuracy = 4.4066369e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
FEP settings ...
temperature = 300.000000
tail no
lj/cut/tip4p/long/soft lambda 1-2 3-4
1-1 charge
2-2 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.17 | 12.18 Mbytes
Step TotEng KinEng PotEng E_vdwl E_coul E_long Temp Press Density v_lambda v_q1 v_q2
0 -3294.6922 648.37071 -3943.0629 689.04498 27082.786 -31717.062 300.435 -1136.6197 0.98149922 1 -0.24 0.06
5000 -3300.0855 688.75259 -3988.8381 720.09187 27007.194 -31718.806 319.14672 -490.2005 0.99596885 0.9975 -0.2394 0.05985
10000 -3331.4444 652.57047 -3984.0149 770.13024 26964.178 -31720.156 302.38103 608.19798 0.9867963 0.995 -0.2388 0.0597
15000 -3317.9366 623.85905 -3941.7956 734.96511 27038.729 -31718.813 289.07705 -68.894551 0.99620066 0.9925 -0.2382 0.05955
20000 -3356.5017 622.48112 -3978.9828 791.34687 26946.421 -31718.414 288.43856 347.88492 0.95690123 0.99 -0.2376 0.0594
25000 -3308.6241 637.21901 -3945.8432 701.68867 27069.809 -31719.744 295.26764 -576.40592 0.97808938 0.9875 -0.237 0.05925
30000 -3268.9616 646.30182 -3915.2635 692.86607 27107.067 -31719.486 299.47633 -627.1163 0.98270296 0.985 -0.2364 0.0591
35000 -3353.5791 627.44774 -3981.0268 715.64502 27018.484 -31720.596 290.73993 -671.96581 0.97562727 0.9825 -0.2358 0.05895
40000 -3366.3894 615.13583 -3981.5252 739.84021 26993.162 -31717.781 285.03498 71.956237 1.0028711 0.98 -0.2352 0.0588
45000 -3278.7772 653.03561 -3931.8128 728.3238 27058.386 -31720.847 302.59657 -204.57499 0.98355616 0.9775 -0.2346 0.05865
50000 -3328.0409 652.01796 -3980.0589 735.50885 26999.996 -31717.026 302.12502 -147.36813 0.99832388 0.975 -0.234 0.0585
55000 -3320.7332 634.51016 -3955.2434 733.31216 27030.192 -31720.582 294.01245 -214.13289 0.97804272 0.9725 -0.2334 0.05835
60000 -3265.0127 649.66719 -3914.6799 717.71007 27084.95 -31719.395 301.03574 -275.84112 0.97721238 0.97 -0.2328 0.0582
65000 -3296.9453 667.09895 -3964.0443 713.15355 27038.116 -31717.446 309.11308 -775.40143 0.9596487 0.9675 -0.2322 0.05805
70000 -3326.8176 610.1396 -3936.9572 759.12327 27019.426 -31720.267 282.71988 386.9984 0.9805237 0.965 -0.2316 0.0579
75000 -3295.6213 619.43931 -3915.0606 744.41867 27057.616 -31720.379 287.02908 160.31549 0.96526127 0.9625 -0.231 0.05775
80000 -3319.0003 642.16787 -3961.1682 698.26556 27056.473 -31718.957 297.56079 -812.57812 0.97915775 0.96 -0.2304 0.0576
85000 -3275.3452 671.73859 -3947.0838 734.53053 27033.862 -31718.806 311.26295 555.74464 1.0247379 0.9575 -0.2298 0.05745
90000 -3353.1322 603.88322 -3957.0155 762.05179 26995.621 -31717.378 279.82086 84.455754 0.97122429 0.955 -0.2292 0.0573
95000 -3310.0949 630.02684 -3940.1218 661.29743 27115.782 -31720.067 291.93501 -1117.7295 0.99837384 0.9525 -0.2286 0.05715
100000 -3287.7733 633.81565 -3921.5889 687.00844 27108.543 -31719.948 293.69063 -1082.8287 0.97122457 0.95 -0.228 0.057
105000 -3320.9973 642.25999 -3963.2573 771.15562 26984.002 -31720.37 297.60348 494.27724 0.97939567 0.9475 -0.2274 0.05685
110000 -3271.2503 682.46763 -3953.7179 717.72459 27040.506 -31715.648 316.23446 139.98334 1.0061057 0.945 -0.2268 0.0567
115000 -3230.6271 657.8128 -3888.4399 704.94943 27121.81 -31718.884 304.81017 -175.18562 0.98938679 0.9425 -0.2262 0.05655
120000 -3354.4761 646.55896 -4001.0351 737.80008 26979.08 -31719.117 299.59549 -687.78242 0.97356203 0.94 -0.2256 0.0564
125000 -3307.9326 651.94271 -3959.8753 767.93628 26986.225 -31715.772 302.09015 674.48659 0.99075217 0.9375 -0.225 0.05625
130000 -3252.6616 653.33949 -3906.0011 737.70688 27069.103 -31715.61 302.73737 61.502238 0.95074576 0.935 -0.2244 0.0561
135000 -3337.2068 624.11194 -3961.3188 726.10143 27027.534 -31718.691 289.19423 -399.06739 0.975193 0.9325 -0.2238 0.05595
140000 -3273.2993 650.03446 -3923.3337 722.58849 27068.141 -31718.93 301.20593 109.7555 1.0125164 0.93 -0.2232 0.0558
145000 -3361.1844 630.1629 -3991.3473 761.22674 26960.945 -31717.903 291.99806 98.529698 0.9842552 0.9275 -0.2226 0.05565
150000 -3397.6956 620.04439 -4017.74 769.23302 26927.291 -31716.976 287.30945 -4.6260994 0.98671248 0.925 -0.222 0.0555
155000 -3324.2698 633.84999 -3958.1198 762.57412 26996.897 -31721.318 293.70654 548.34435 0.98920982 0.9225 -0.2214 0.05535
160000 -3343.9484 643.52355 -3987.4719 759.58357 26968.943 -31717.703 298.18897 -14.622864 0.98634427 0.92 -0.2208 0.0552
165000 -3312.27 638.38126 -3950.6513 734.66797 27029.589 -31718.628 295.80619 -278.68476 0.97131029 0.9175 -0.2202 0.05505
170000 -3304.1638 653.71924 -3957.883 758.71859 26998.407 -31717.699 302.91334 556.6553 0.99062914 0.915 -0.2196 0.0549
175000 -3348.5751 636.35096 -3984.926 716.66884 27013.923 -31719.395 294.86542 -493.93923 1.0094499 0.9125 -0.219 0.05475
180000 -3314.3089 642.35345 -3956.6623 746.03994 27014.289 -31719.309 297.64678 18.793089 0.98688216 0.91 -0.2184 0.0546
185000 -3305.5307 656.49472 -3962.0254 698.68453 27053.976 -31718.699 304.19941 -655.04866 0.9953262 0.9075 -0.2178 0.05445
190000 -3319.0075 628.14762 -3947.1551 760.10501 27010.832 -31719.877 291.06424 495.59849 0.99024489 0.905 -0.2172 0.0543
195000 -3359.1251 645.3591 -4004.4842 706.03177 27003.968 -31717.297 299.03951 -987.2232 1.0030744 0.9025 -0.2166 0.05415
200000 -3265.1994 653.17314 -3918.3725 745.43252 27051.185 -31716.468 302.66029 492.87431 0.98271789 0.9 -0.216 0.054
205000 -3326.7435 634.62415 -3961.3677 733.67518 27021.402 -31718.37 294.06526 -610.98205 0.97647098 0.8975 -0.2154 0.05385
210000 -3341.4069 629.61701 -3971.0239 788.26956 26951.424 -31717.953 291.74511 784.09039 0.98181574 0.895 -0.2148 0.0537
215000 -3328.6327 629.18147 -3957.8142 741.68875 27018.252 -31720.903 291.54329 -389.24921 0.97384889 0.8925 -0.2142 0.05355
220000 -3330.2335 631.1408 -3961.3743 711.41512 27041.269 -31717.027 292.45119 -529.07456 0.99951453 0.89 -0.2136 0.0534
225000 -3279.1467 651.38387 -3930.5306 675.7848 27109.317 -31717.64 301.8312 -1355.4842 0.97063846 0.8875 -0.213 0.05325
230000 -3258.5618 674.19802 -3932.7598 696.46848 27086.441 -31719.629 312.40257 -798.15463 0.98875283 0.885 -0.2124 0.0531
235000 -3301.5452 661.5648 -3963.11 760.55878 26993.336 -31718.61 306.54873 388.65302 0.98559781 0.8825 -0.2118 0.05295
240000 -3260.292 688.11931 -3948.4113 796.99706 26969.933 -31716.82 318.85327 1273.6638 0.98971045 0.88 -0.2112 0.0528
245000 -3335.2668 650.00152 -3985.2683 732.51438 26997.569 -31719.222 301.19066 -527.33325 0.97446562 0.8775 -0.2106 0.05265
250000 -3335.3004 634.43787 -3969.7383 693.40008 27051.388 -31715.921 293.97895 -775.65835 0.997393 0.875 -0.21 0.0525
255000 -3308.9727 644.64293 -3953.6156 775.97061 26985.278 -31718.351 298.70766 735.72268 0.97151151 0.8725 -0.2094 0.05235
260000 -3377.5078 607.25295 -3984.7607 756.34352 26972.957 -31717.896 281.3823 421.20354 0.99480934 0.87 -0.2088 0.0522
265000 -3332.2782 635.01747 -3967.2957 774.98012 26971.131 -31718.281 294.24751 542.48287 0.9953591 0.8675 -0.2082 0.05205
270000 -3300.1877 666.69132 -3966.879 740.28005 27005.011 -31716.98 308.9242 324.45834 1.010532 0.865 -0.2076 0.0519
275000 -3310.6523 656.2584 -3966.9107 742.16026 27009.436 -31720.438 304.08991 -39.601026 0.99637116 0.8625 -0.207 0.05175
280000 -3267.8018 673.29725 -3941.0991 718.41223 27057.428 -31719.711 311.98519 -199.35683 0.99136443 0.86 -0.2064 0.0516
285000 -3331.8267 646.80574 -3978.6324 741.20142 26993.85 -31717.481 299.70984 -196.98987 0.98711039 0.8575 -0.2058 0.05145
290000 -3290.9098 646.64126 -3937.551 712.52482 27064.101 -31718.746 299.63362 -716.1483 0.9903895 0.855 -0.2052 0.0513
295000 -3292.3147 648.30694 -3940.6216 758.36829 27014.672 -31717.725 300.40545 146.02666 0.9770053 0.8525 -0.2046 0.05115
300000 -3300.7153 652.90614 -3953.6214 717.51899 27044.806 -31718.801 302.53657 -465.46422 0.98995271 0.85 -0.204 0.051
305000 -3302.312 661.21204 -3963.524 769.72588 26984.217 -31719.384 306.38527 592.72331 0.99013085 0.8475 -0.2034 0.05085
310000 -3288.3629 640.87702 -3929.24 754.52854 27032.351 -31719.089 296.96265 -222.18249 0.95794412 0.845 -0.2028 0.0507
315000 -3288.0534 665.74093 -3953.7943 747.86808 27017.145 -31719.985 308.48382 187.10954 0.98643537 0.8425 -0.2022 0.05055
320000 -3334.9572 637.5192 -3972.4764 787.9527 26953.042 -31717.487 295.40674 855.44588 0.98641732 0.84 -0.2016 0.0504
325000 -3356.6357 660.59505 -4017.2307 716.63049 26981.051 -31717.236 306.09938 -809.64248 0.99818007 0.8375 -0.201 0.05025
330000 -3352.7362 640.12342 -3992.8596 820.05526 26903.626 -31719.646 296.61346 1388.801 1.0088247 0.835 -0.2004 0.0501
335000 -3274.3109 658.23471 -3932.5456 760.70544 27023.794 -31720.422 305.00567 407.72655 0.98774503 0.8325 -0.1998 0.04995
340000 -3354.4542 630.85037 -3985.3046 751.482 26980.613 -31718.962 292.31661 -5.4828109 0.99096195 0.83 -0.1992 0.0498
345000 -3255.206 641.38727 -3896.5933 725.02817 27090.417 -31716.022 297.19908 582.06745 0.99135711 0.8275 -0.1986 0.04965
350000 -3300.5992 659.81325 -3960.4125 756.1521 26998.118 -31718.581 305.73712 -15.759793 0.9852493 0.825 -0.198 0.0495
355000 -3272.7741 673.31115 -3946.0853 724.9325 27041.246 -31716.53 311.99163 -465.84023 0.98346796 0.8225 -0.1974 0.04935
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1650000 -3321.3309 649.53534 -3970.8662 777.01324 26966.538 -31717.763 300.97465 108.71811 0.977065 0.175 -0.042 0.0105
1655000 -3403.4099 624.4219 -4027.8318 784.1127 26901.103 -31715.332 289.33786 68.508642 0.98072121 0.1725 -0.0414 0.01035
1660000 -3322.9984 664.06939 -3987.0678 731.71583 26995.436 -31716.834 307.70928 -332.14967 1.0025238 0.17 -0.0408 0.0102
1665000 -3230.6744 674.72794 -3905.4023 778.68595 27028.003 -31714.516 312.64812 1375.7415 0.99106584 0.1675 -0.0402 0.01005
1670000 -3290.79 637.69021 -3928.4802 700.32081 27081.091 -31712.466 295.48598 -1069.0971 0.96641143 0.165 -0.0396 0.0099
1675000 -3305.5875 621.22384 -3926.8113 695.99742 27090.166 -31715.288 287.85597 -1077.693 0.97177543 0.1625 -0.039 0.00975
1680000 -3268.9563 666.32635 -3935.2826 731.88233 27044.222 -31713.791 308.75509 -292.28331 0.97523238 0.16 -0.0384 0.0096
1685000 -3265.1149 639.41443 -3904.5293 721.62746 27086.503 -31716.035 296.28493 128.76044 0.99772509 0.1575 -0.0378 0.00945
1690000 -3326.8204 620.81306 -3947.6335 711.91766 27051.866 -31714.515 287.66563 -454.38876 0.98740179 0.155 -0.0372 0.0093
1695000 -3323.3897 684.06584 -4007.4555 744.82803 26961.661 -31715.201 316.97502 -679.14465 0.98094411 0.1525 -0.0366 0.00915
1700000 -3294.5706 653.01083 -3947.5814 781.85245 26983.199 -31713.887 302.58508 502.73081 0.97555506 0.15 -0.036 0.009
1705000 -3262.6576 685.19558 -3947.8532 757.26837 27012.265 -31718.135 317.49851 199.86853 0.97458873 0.1475 -0.0354 0.00885
1710000 -3255.8527 664.21235 -3920.065 703.16733 27091.894 -31717.024 307.77552 -355.94123 0.98084795 0.145 -0.0348 0.0087
1715000 -3287.5581 663.07942 -3950.6375 745.7211 27017.25 -31716.816 307.25056 114.0679 0.98657314 0.1425 -0.0342 0.00855
1720000 -3288.8458 658.50053 -3947.3463 690.29419 27077.889 -31717.344 305.12884 -1077.3116 0.98627147 0.14 -0.0336 0.0084
1725000 -3256.8223 656.34601 -3913.1683 768.47754 27032.602 -31715.721 304.1305 1023.5837 1.0029652 0.1375 -0.033 0.00825
1730000 -3346.7551 634.38611 -3981.1412 787.69666 26941.51 -31713.373 293.95496 464.32109 1.0083983 0.135 -0.0324 0.0081
1735000 -3294.4857 631.50013 -3925.9858 797.15264 26989.537 -31715.081 292.61769 835.64006 0.97238705 0.1325 -0.0318 0.00795
1740000 -3277.7412 645.9919 -3923.7331 727.45728 27061.304 -31714.776 299.33273 250.78941 0.9991219 0.13 -0.0312 0.0078
1745000 -3197.3765 716.79028 -3914.1668 734.244 27064.614 -31716.712 332.13851 19.166712 0.98333244 0.1275 -0.0306 0.00765
1750000 -3280.6313 622.07639 -3902.7076 700.86328 27106.933 -31712.398 288.25102 -658.71601 0.96809002 0.125 -0.03 0.0075
1755000 -3353.4925 658.66227 -4012.1548 757.72466 26942.913 -31715.245 305.20379 -343.411 0.98054785 0.1225 -0.0294 0.00735
1760000 -3269.008 691.45617 -3960.4641 748.05619 27002.818 -31713.225 320.39947 -167.78778 0.9720822 0.12 -0.0288 0.0072
1765000 -3312.1326 611.95973 -3924.0924 757.47097 27030.715 -31714.571 283.56327 594.93622 0.99970232 0.1175 -0.0282 0.00705
1770000 -3286.3959 628.16202 -3914.5579 717.36235 27083.618 -31717.665 291.07091 -696.94933 0.96376643 0.115 -0.0276 0.0069
1775000 -3349.2898 646.78418 -3996.0739 788.07114 26929.998 -31716.612 299.69985 582.27147 0.99837139 0.1125 -0.027 0.00675
1780000 -3347.1791 641.46049 -3988.6396 771.25773 26949.128 -31712.171 297.23301 78.03711 0.98201965 0.11 -0.0264 0.0066
1785000 -3399.4313 609.86503 -4009.2964 774.22094 26930.236 -31715.572 282.59265 18.158627 0.99130491 0.1075 -0.0258 0.00645
1790000 -3256.2797 680.01538 -3936.2951 772.26827 27002.742 -31713.66 315.09816 310.40267 0.97426571 0.105 -0.0252 0.0063
1795000 -3235.4884 688.93945 -3924.4278 732.98748 27057.009 -31716.446 319.2333 331.09084 1.0121548 0.1025 -0.0246 0.00615
1800000 -3219.9708 706.2187 -3926.1895 718.33138 27063.848 -31711.164 327.23997 -296.07765 0.98975934 0.1 -0.024 0.006
1805000 -3347.4225 630.49902 -3977.9215 790.79036 26943.342 -31714.525 292.15381 806.57337 0.98493764 0.0975 -0.0234 0.00585
1810000 -3316.95 672.66189 -3989.6119 701.96639 27021.379 -31715.012 311.69078 -1055.3668 0.98445711 0.095 -0.0228 0.0057
1815000 -3271.6474 640.25549 -3911.9029 731.4301 27070.097 -31714.358 296.67465 235.37666 1.0034769 0.0925 -0.0222 0.00555
1820000 -3268.5852 680.254 -3948.8392 698.09264 27066.868 -31716.458 315.20873 -1109.4344 0.96597756 0.09 -0.0216 0.0054
1825000 -3262.9465 630.22321 -3893.1697 726.12284 27094.819 -31716.584 292.026 581.49063 1.0165405 0.0875 -0.021 0.00525
1830000 -3325.4078 638.0573 -3963.4651 756.40841 26993.12 -31714.702 295.65608 457.52139 1.0060574 0.085 -0.0204 0.0051
1835000 -3290.2308 674.15556 -3964.3864 765.51879 26983.211 -31715.658 312.3829 413.34394 0.99030238 0.0825 -0.0198 0.00495
1840000 -3293.6063 667.63971 -3961.246 762.12518 26989.509 -31714.815 309.36366 251.72168 0.98152944 0.08 -0.0192 0.0048
1845000 -3284.2343 648.29591 -3932.5302 699.15751 27081.807 -31715.665 300.40034 -775.34257 0.98697792 0.0775 -0.0186 0.00465
1850000 -3318.1752 650.0401 -3968.2153 754.30022 26990.44 -31715.971 301.20854 31.798924 0.99366234 0.075 -0.018 0.0045
1855000 -3306.6157 643.15276 -3949.7685 706.55721 27057.479 -31715.55 298.01716 -517.28002 1.0016605 0.0725 -0.0174 0.00435
1860000 -3338.5777 667.1098 -4005.6875 791.29942 26914.244 -31714.244 309.11811 255.63501 0.9776517 0.07 -0.0168 0.0042
1865000 -3255.8144 682.49145 -3938.3059 787.02607 26989.795 -31716.255 316.24549 1264.0634 0.99887736 0.0675 -0.0162 0.00405
1870000 -3252.5858 652.25726 -3904.843 728.41299 27078.64 -31714.713 302.2359 -144.5641 0.96491991 0.065 -0.0156 0.0039
1875000 -3309.5832 657.30055 -3966.8837 757.25255 26988.913 -31716.067 304.57281 -98.604822 0.97743277 0.0625 -0.015 0.00375
1880000 -3291.493 627.19859 -3918.6916 813.07962 26981.192 -31715.581 290.62449 1806.5676 0.99104762 0.06 -0.0144 0.0036
1885000 -3281.941 687.05046 -3968.9915 763.18602 26982.454 -31716.979 318.358 417.67646 0.98625193 0.0575 -0.0138 0.00345
1890000 -3341.5498 656.97914 -3998.5289 745.15547 26970.163 -31715.423 304.42388 -504.08068 0.98243229 0.055 -0.0132 0.0033
1895000 -3301.6893 646.54019 -3948.2295 755.23573 27006.885 -31712.598 299.58679 376.14539 1.0048319 0.0525 -0.0126 0.00315
1900000 -3311.333 679.67795 -3991.011 789.29593 26931.648 -31715.122 314.9418 1037.345 1.0008807 0.05 -0.012 0.003
1905000 -3272.5003 668.40254 -3940.9029 718.08609 27055.948 -31716.781 309.71713 -286.48891 0.9881103 0.0475 -0.0114 0.00285
1910000 -3316.0584 632.02506 -3948.0835 717.60788 27049.658 -31715.89 292.86092 -677.83531 0.97723045 0.045 -0.0108 0.0027
1915000 -3290.6575 648.69049 -3939.348 758.99479 27016.633 -31716.858 300.58317 246.76601 0.96014992 0.0425 -0.0102 0.00255
1920000 -3337.0208 654.36708 -3991.3879 778.3941 26944.246 -31716.56 303.21353 139.89699 0.97481392 0.04 -0.0096 0.0024
1925000 -3308.835 651.31942 -3960.1544 747.1061 27005.987 -31715.946 301.80134 198.017 1.0050256 0.0375 -0.009 0.00225
1930000 -3267.2823 650.37412 -3917.6564 687.99454 27106.599 -31714.928 301.36332 -1038.4201 1.0011545 0.035 -0.0084 0.0021
1935000 -3236.5517 660.79742 -3897.3492 735.17944 27080.865 -31714.98 306.19315 447.84091 0.98014234 0.0325 -0.0078 0.00195
1940000 -3302.0749 666.44585 -3968.5207 714.39673 27032.752 -31716.425 308.81046 -473.87926 0.99447376 0.03 -0.0072 0.0018
1945000 -3289.2027 649.86308 -3939.0658 768.49924 27007.675 -31717.121 301.12651 762.21746 0.99009954 0.0275 -0.0066 0.00165
1950000 -3302.329 674.76941 -3977.0984 747.09562 26989.466 -31715.313 312.66734 54.832799 0.98726677 0.025 -0.006 0.0015
1955000 -3374.3031 630.83296 -4005.136 748.81361 26958.785 -31714.835 292.30855 -55.126833 1.0060118 0.0225 -0.0054 0.00135
1960000 -3310.8401 650.42767 -3961.2678 698.49943 27052.7 -31715.642 301.38813 -934.48079 0.99288724 0.02 -0.0048 0.0012
1965000 -3322.5064 642.37053 -3964.8769 716.05096 27034.95 -31717.88 297.6547 -665.83966 0.99509011 0.0175 -0.0042 0.00105
1970000 -3342.4338 651.08011 -3993.5139 736.17906 26984.325 -31715.44 301.69045 -270.5898 1.0014792 0.015 -0.0036 0.0009
1975000 -3214.2892 674.99303 -3889.2823 709.11194 27114.071 -31714.739 312.77096 -484.54747 0.97382166 0.0125 -0.003 0.00075
1980000 -3295.588 655.21711 -3950.8051 774.69267 26985.789 -31714.898 303.60741 87.748457 0.97621381 0.01 -0.0024 0.0006
1985000 -3294.657 629.82765 -3924.4846 768.55597 27021.837 -31717.283 291.84272 954.88617 1.0050703 0.0075 -0.0018 0.00045
1990000 -3257.912 660.54527 -3918.4573 722.75762 27072.838 -31716.199 306.07631 -423.44025 0.97598965 0.005 -0.0012 0.0003
1995000 -3329.3158 619.57927 -3948.8951 741.75692 27023.601 -31715.502 287.09393 82.743609 0.98909553 0.0025 -0.0006 0.00015
2000000 -3319.1334 640.84972 -3959.9831 743.80101 27008.342 -31715.397 296.95 -195.97682 0.9873309 0 -0 0
Loop time of 14364.3 on 12 procs for 2000000 steps with 1085 atoms
Performance: 12.030 ns/day, 1.995 hours/ns, 139.234 timesteps/s
97.0% CPU use with 12 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9160.5 | 9644 | 10300 | 337.6 | 67.14
Bond | 1.9786 | 2.3327 | 2.6679 | 14.1 | 0.02
Kspace | 2352.2 | 3005.6 | 3482.9 | 601.4 | 20.92
Neigh | 203.66 | 204.21 | 204.86 | 2.5 | 1.42
Comm | 558.29 | 619.37 | 646.39 | 129.0 | 4.31
Output | 0.086027 | 0.087123 | 0.094828 | 0.8 | 0.00
Modify | 612.7 | 688.57 | 844.5 | 339.7 | 4.79
Other | | 200.1 | | | 1.39
Nlocal: 90.4167 ave 102 max 80 min
Histogram: 1 2 0 3 0 2 1 1 1 1
Nghost: 3928.08 ave 3982 max 3886 min
Histogram: 2 1 2 1 1 1 2 0 0 2
Neighs: 0.833333 ave 9 max 0 min
Histogram: 10 1 0 0 0 0 0 0 0 1
Total # of neighbors = 10
Ave neighs/atom = 0.0092165899
Ave special neighs/atom = 2.0092166
Neighbor list builds = 80758
Dangerous builds = 0
# write_restart restart.*.lmp
write_data data.*.lmp
System init for write_data ...
PPPM initialization ...
extracting TIP4P info from pair style
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.28572351
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.014544301
estimated relative force accuracy = 4.3799731e-05
using double precision FFTW3
3d grid and FFT values/proc = 2352 450
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.25
ghost atom cutoff = 12.25
binsize = 6.125, bins = 4 4 4
3 neighbor lists, perpetual/occasional/extra = 3 0 0
(1) pair lj/cut/coul/long, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(2) pair lj/cut/tip4p/long/soft, perpetual, skip from (3)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) neighbor class addition, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Total wall time: 4:10:34

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compute fep examples
====================
* `CH4hyd` -- free energy of hydration of methane (very simple). FEP
and TI methods.
* `CH4-CF4` -- free energy difference of transforming methane into
perfluoromethane, in water (simple). BAR method.
* `CC-CO` -- free energy difference of transforming ethane into
methanol, in water (more complex). FEP, TI and BAR methods.
* 'C7inEthanol' -- insertion / deletion of a hexane molecule in ethanol.
The hexane is described by the lj/class2/coul/long/soft potential.

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compute fep examples
====================
The examples below illustrate the use of *compute fep*, *fix adapt/fep* and
*pair lj/cut/coul/long/soft* to calculate free energy differences. They present
just one version of many possible ways of constructing a path from the initial
to the final states.
* `CH4hyd` -- free energy of hydration of methane (simple). FEP
and FDTI methods.
* `CH4-CF4` -- free energy difference of transforming methane into
perfluoromethane, in water (quite simple). FEP and BAR methods.
* `CC-CO` -- hydration free energy difference between ethane and methanol
(a bit more complex). FEP method.
* `C7inEthanol` -- insertion / deletion of a hexane molecule in ethanol.
The hexane is described by the *lj/class2/coul/long/soft* potential.
* `quicktests` -- very short runs with charged Lennard-Jones atoms to test
*compute fep*, *fix adapt/fep* and *pair lj/cut/coul/long/soft*.

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# two LJ particles
units real
boundary p p p
atom_style charge
pair_style lj/cut/coul/long/soft 1.0 0.0 0.0 12.0 12.0
region box block -15.0 15.0 -15.0 15.0 -15.0 15.0
create_box 2 box
# just two atoms...
#create_atoms 1 single 0.0 0.0 0.0
## create_atoms 2 single 3.36738 0.0 0.0
#create_atoms 2 single 6.0 0.0 0.0
# ...or a few on a lattice
lattice bcc 5.0
create_atoms 1 box basis 1 1 basis 2 2
mass 1 12.011
mass 2 12.011
pair_coeff 1 1 0.1 3.0 1.0
pair_coeff 1 2 0.1 3.0 1.0
pair_coeff 2 2 0.1 3.0 1.0
set type 1 charge 0.1
set type 2 charge -0.1
kspace_style pppm 1.0e-5
timestep 2.0
velocity all create 300.0 12345
fix INTEG all nvt temp 300.0 300.0 $(100.0*dt)
variable lam equal ramp(1.0,0.0)
variable q1 equal 0.1*v_lam
variable q2 equal -0.1*v_lam
fix ADAPT all adapt/fep 200 &
pair lj/cut/coul/long/soft lambda * * v_lam &
atom charge 1 v_q1 atom charge 2 v_q2
thermo_style custom step etotal ke pe epair evdwl ecoul elong temp press v_lam v_q1 v_q2
thermo 200
#dump TRAJ all custom 20 dump.lammpstrj id type element xu yu zu
#dump_modify TRAJ element C N
run 2000
#write_data data.*.lmp

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# two LJ particles
units real
boundary p p p
atom_style charge
pair_style lj/cut/coul/long/soft 1.0 0.0 0.0 12.0 12.0
region box block -15.0 15.0 -15.0 15.0 -15.0 15.0
create_box 2 box
# just two atoms...
#create_atoms 1 single 0.0 0.0 0.0
## create_atoms 2 single 3.36738 0.0 0.0
#create_atoms 2 single 6.0 0.0 0.0
# ...or a few on a lattice
lattice bcc 5.0
create_atoms 1 box basis 1 1 basis 2 2
mass 1 12.011
mass 2 12.011
pair_coeff 1 1 0.1 3.0 1.0
pair_coeff 1 2 0.1 3.0 1.0
pair_coeff 2 2 0.1 3.0 1.0
set type 1 charge 0.1
set type 2 charge -0.1
kspace_style pppm 1.0e-5
timestep 2.0
velocity all create 300.0 12345
fix INTEG all nvt temp 300.0 300.0 $(100.0*dt)
variable dlam equal -0.1
variable dq equal -0.01
variable mdq equal -v_dq
compute FEP all fep 300.0 &
pair lj/cut/coul/long/soft lambda * * v_dlam &
atom charge 1 v_dq atom charge 2 v_mdq
variable diff equal "0.1*evdwl + (1.0-0.9^3)*ecoul + (1.0-0.9^2)*elong + c_FEP[1]"
thermo_style custom step etotal epair evdwl ecoul elong temp press c_FEP[1] v_diff
thermo 200
#dump TRAJ all custom 20 dump.lammpstrj id type element xu yu zu
#dump_modify TRAJ element C N
run 2000
#write_data data.*.lmp

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LAMMPS (10 Feb 2021)
# two LJ particles
units real
boundary p p p
atom_style charge
pair_style lj/cut/coul/long/soft 1.0 0.0 0.0 12.0 12.0
region box block -15.0 15.0 -15.0 15.0 -15.0 15.0
create_box 2 box
Created orthogonal box = (-15.000000 -15.000000 -15.000000) to (15.000000 15.000000 15.000000)
1 by 1 by 1 MPI processor grid
# just two atoms...
#create_atoms 1 single 0.0 0.0 0.0
## create_atoms 2 single 3.36738 0.0 0.0
#create_atoms 2 single 6.0 0.0 0.0
# ...or a few on a lattice
lattice bcc 5.0
Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
create_atoms 1 box basis 1 1 basis 2 2
Created 432 atoms
create_atoms CPU = 0.000 seconds
mass 1 12.011
mass 2 12.011
pair_coeff 1 1 0.1 3.0 1.0
pair_coeff 1 2 0.1 3.0 1.0
pair_coeff 2 2 0.1 3.0 1.0
set type 1 charge 0.1
Setting atom values ...
216 settings made for charge
set type 2 charge -0.1
Setting atom values ...
216 settings made for charge
kspace_style pppm 1.0e-5
timestep 2.0
velocity all create 300.0 12345
fix INTEG all nvt temp 300.0 300.0 $(100.0*dt)
fix INTEG all nvt temp 300.0 300.0 200
variable lam equal ramp(1.0,0.0)
variable q1 equal 0.1*v_lam
variable q2 equal -0.1*v_lam
fix ADAPT all adapt/fep 200 pair lj/cut/coul/long/soft lambda * * v_lam atom charge 1 v_q1 atom charge 2 v_q2
thermo_style custom step etotal ke pe epair evdwl ecoul elong temp press v_lam v_q1 v_q2
thermo 200
#dump TRAJ all custom 20 dump.lammpstrj id type element xu yu zu
#dump_modify TRAJ element C N
run 2000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.18385633
grid = 8 8 8
stencil order = 5
estimated absolute RMS force accuracy = 0.0026371085
estimated relative force accuracy = 7.9415739e-06
using double precision FFTW3
3d grid and FFT values/proc = 2197 512
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long/soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.832 | 3.832 | 3.832 Mbytes
Step TotEng KinEng PotEng E_pair E_vdwl E_coul E_long Temp Press v_lam v_q1 v_q2
0 -12.26816 385.41874 -397.6869 -397.6869 -104.94426 -143.9636 -148.77903 300 -85.376499 1 0.1 -0.1
200 100.16354 367.45985 -267.29631 -267.29631 -81.614062 -73.094016 -112.58823 286.02127 773.38887 0.9 0.09 -0.09
400 212.21213 408.60204 -196.38992 -196.38992 -61.139783 -47.980995 -87.269141 318.04529 999.04315 0.8 0.08 -0.08
600 236.48535 384.11175 -147.6264 -147.6264 -50.471465 -30.008006 -67.146932 298.98267 991.19571 0.7 0.07 -0.07
800 296.13924 393.67656 -97.537322 -97.537322 -35.286021 -14.501948 -47.749352 306.42767 1072.3208 0.6 0.06 -0.06
1000 321.41212 388.66588 -67.253761 -67.253761 -27.633917 -7.5804948 -32.03935 302.52749 1042.921 0.5 0.05 -0.05
1200 361.76959 401.68937 -39.919779 -39.919779 -18.818919 -2.1433883 -18.957472 312.66464 1024.5985 0.4 0.04 -0.04
1400 378.95801 397.71207 -18.754062 -18.754062 -8.3450648 -0.50003204 -9.9089656 309.56881 1009.4706 0.3 0.03 -0.03
1600 377.85273 381.94383 -4.0910985 -4.0910985 -0.39457825 -0.054299578 -3.6422206 297.29522 937.1911 0.2 0.02 -0.02
1800 395.79855 387.74178 8.0567724 8.0567724 8.9308992 -0.0096463334 -0.8644804 301.8082 905.24994 0.1 0.01 -0.01
WARNING: Using kspace solver on system with no charge (src/lammps/src/kspace.cpp:311)
2000 395.41984 395.41984 0 0 0 0 0 307.7846 669.46448 0 0 -0
Loop time of 2.57067 on 1 procs for 2000 steps with 432 atoms
Performance: 134.439 ns/day, 0.179 hours/ns, 778.006 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.11 | 2.11 | 2.11 | 0.0 | 82.08
Kspace | 0.34475 | 0.34475 | 0.34475 | 0.0 | 13.41
Neigh | 0.074478 | 0.074478 | 0.074478 | 0.0 | 2.90
Comm | 0.023527 | 0.023527 | 0.023527 | 0.0 | 0.92
Output | 0.000318 | 0.000318 | 0.000318 | 0.0 | 0.01
Modify | 0.012899 | 0.012899 | 0.012899 | 0.0 | 0.50
Other | | 0.004675 | | | 0.18
Nlocal: 432.000 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2702.00 ave 2702 max 2702 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39560.0 ave 39560 max 39560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39560
Ave neighs/atom = 91.574074
Neighbor list builds = 66
Dangerous builds = 0
#write_data data.*.lmp
Total wall time: 0:00:02

135
examples/USER/fep/quicktests/log.fep_soft Normal file
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@ -0,0 +1,135 @@
LAMMPS (10 Feb 2021)
# two LJ particles
units real
boundary p p p
atom_style charge
pair_style lj/cut/coul/long/soft 1.0 0.0 0.0 12.0 12.0
region box block -15.0 15.0 -15.0 15.0 -15.0 15.0
create_box 2 box
Created orthogonal box = (-15.000000 -15.000000 -15.000000) to (15.000000 15.000000 15.000000)
1 by 1 by 1 MPI processor grid
# just two atoms...
#create_atoms 1 single 0.0 0.0 0.0
## create_atoms 2 single 3.36738 0.0 0.0
#create_atoms 2 single 6.0 0.0 0.0
# ...or a few on a lattice
lattice bcc 5.0
Lattice spacing in x,y,z = 5.0000000 5.0000000 5.0000000
create_atoms 1 box basis 1 1 basis 2 2
Created 432 atoms
create_atoms CPU = 0.000 seconds
mass 1 12.011
mass 2 12.011
pair_coeff 1 1 0.1 3.0 1.0
pair_coeff 1 2 0.1 3.0 1.0
pair_coeff 2 2 0.1 3.0 1.0
set type 1 charge 0.1
Setting atom values ...
216 settings made for charge
set type 2 charge -0.1
Setting atom values ...
216 settings made for charge
kspace_style pppm 1.0e-5
timestep 2.0
velocity all create 300.0 12345
fix INTEG all nvt temp 300.0 300.0 $(100.0*dt)
fix INTEG all nvt temp 300.0 300.0 200
variable dlam equal -0.1
variable dq equal -0.01
variable mdq equal -v_dq
compute FEP all fep 300.0 pair lj/cut/coul/long/soft lambda * * v_dlam atom charge 1 v_dq atom charge 2 v_mdq
variable diff equal "0.1*evdwl + (1.0-0.9^3)*ecoul + (1.0-0.9^2)*elong + c_FEP[1]"
thermo_style custom step etotal epair evdwl ecoul elong temp press c_FEP[1] v_diff
thermo 200
#dump TRAJ all custom 20 dump.lammpstrj id type element xu yu zu
#dump_modify TRAJ element C N
run 2000
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/lammps/src/kspace.cpp:339)
G vector (1/distance) = 0.18385633
grid = 8 8 8
stencil order = 5
estimated absolute RMS force accuracy = 0.0026371085
estimated relative force accuracy = 7.9415739e-06
using double precision FFTW3
3d grid and FFT values/proc = 2197 512
FEP settings ...
temperature = 300.000000
tail no
lj/cut/coul/long/soft lambda 1-2 1-2
1-1 charge
2-2 charge
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut/coul/long/soft, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.832 | 3.832 | 3.832 Mbytes
Step TotEng E_pair E_vdwl E_coul E_long Temp Press c_FEP[1] v_diff
0 -12.26816 -397.6869 -104.94426 -143.9636 -148.77903 300 -85.376499 77.776579 1.8999913e-11
200 37.48027 -329.94625 -90.682292 -100.26614 -138.99782 285.99532 753.55244 62.649939 -3.2116532e-12
400 90.468672 -316.02846 -73.92701 -103.34631 -138.75514 316.40687 1029.3728 61.763027 -2.3732127e-12
600 51.256072 -323.62945 -73.949374 -108.09188 -141.5882 291.80122 1016.7465 63.589594 -2.4300562e-12
800 81.04264 -324.43236 -81.254005 -105.21556 -137.9628 315.61128 993.70961 62.851749 -2.4016344e-12
1000 49.737002 -317.2545 -83.027749 -96.415828 -137.81092 285.65671 868.03876 60.615539 -3.3111291e-12
1200 75.239535 -312.294 -70.8241 -102.021 -139.4489 301.6461 1070.4194 61.225392 -3.0198066e-12
1400 66.48368 -328.58216 -82.267016 -106.59484 -139.72031 307.50906 929.51913 63.660761 -2.4300562e-12
1600 44.171107 -313.98549 -64.634967 -109.51577 -139.83476 278.77985 1072.9026 62.710873 -2.9558578e-12
1800 75.795844 -307.72311 -70.578314 -98.507621 -138.63717 298.52125 1093.0178 60.094459 -3.3395509e-12
2000 66.677947 -312.73751 -69.196548 -104.10753 -139.43342 295.3272 1084.1493 61.625147 -1.5489832e-12
Loop time of 2.63335 on 1 procs for 2000 steps with 432 atoms
Performance: 131.240 ns/day, 0.183 hours/ns, 759.488 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1575 | 2.1575 | 2.1575 | 0.0 | 81.93
Kspace | 0.35767 | 0.35767 | 0.35767 | 0.0 | 13.58
Neigh | 0.076131 | 0.076131 | 0.076131 | 0.0 | 2.89
Comm | 0.023625 | 0.023625 | 0.023625 | 0.0 | 0.90
Output | 0.000348 | 0.000348 | 0.000348 | 0.0 | 0.01
Modify | 0.012821 | 0.012821 | 0.012821 | 0.0 | 0.49
Other | | 0.005206 | | | 0.20
Nlocal: 432.000 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2673.00 ave 2673 max 2673 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39631.0 ave 39631 max 39631 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39631
Ave neighs/atom = 91.738426
Neighbor list builds = 68
Dangerous builds = 0
#write_data data.*.lmp
Total wall time: 0:00:02

2
examples/USER/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
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@ -22,7 +22,7 @@ improper_style class2
read_data tiny_nylon.data
variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5
velocity all create 300.0 4928459 dist gaussian