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update to USER-FEP docs and examples

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This commit is contained in:
Axel Kohlmeyer
2015-05-15 00:59:50 -04:00
parent f084911239
commit 21db4bc68c
15 changed files with 10766 additions and 20422 deletions
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2
doc/Section_packages.txt
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@ -119,7 +119,7 @@ USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sd
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, - USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "fix adapt/fep"_fix_adapt.html, USER/fep, -, - USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, - USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, - USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, - USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -

2
doc/compute_fep.txt
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@ -23,7 +23,7 @@ attribute = {pair} or {atom} :l
I,J = type pair(s) to set parameter for I,J = type pair(s) to set parameter for
v_delta = variable with perturbation to apply (in the units of the parameter) v_delta = variable with perturbation to apply (in the units of the parameter)
{atom} args = aparam I v_delta {atom} args = aparam I v_delta
aparam = parameter to adapt over time aparam = parameter to perturb
I = type to set parameter for I = type to set parameter for
v_delta = variable with perturbation to apply (in the units of the parameter) :pre v_delta = variable with perturbation to apply (in the units of the parameter) :pre
zero or more keyword/value pairs may be appended :l zero or more keyword/value pairs may be appended :l

86
doc/pair_lj_soft.txt
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@ -106,12 +106,12 @@ pair_coeff 1 1 1.0 9.5 :pre
The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones
and Coulomb potential modified by a soft core, in order to avoid and Coulomb potential modified by a soft core, in order to avoid
singularities during free energy calculations when sites are created singularities during free energy calculations when sites are created
or anihilated "(Beutler)"_#Beutler. or anihilated "(Beutler)"_#Beutler,
:c,image(Eqs/pair_lj_soft.jpg) :c,image(Eqs/pair_lj_soft.jpg)
Coulomb interactions are also damped with a soft core at short Coulomb interactions are also damped with a soft core at short
distance as distance,
:c,image(Eqs/pair_coul_soft.jpg) :c,image(Eqs/pair_coul_soft.jpg)
@ -120,11 +120,11 @@ are the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the "dielectric"_dielectric.html command. which can be set by the "dielectric"_dielectric.html command.
The coefficient lambda is an activation parameter. When lambda = 1 the The coefficient lambda is an activation parameter. When lambda = 1 the
pair potentiel is identical to a Lennard-Jones term plus a Coulomb pair potentiel is identical to a Lennard-Jones term or a Coulomb term
term. When lambda = 0 the pair interactions are deactivated. The or a combination of both. When lambda = 0 the interactions are
transition between these two extrema is smoothed by a repulsive soft deactivated. The transition between these two extrema is smoothed by a
core in order to avoid singularities in potential energy and forces soft repulsive core in order to avoid singularities in potential
when sites are created or anihilated and can overlap energy and forces when sites are created or anihilated and can overlap
"(Beutler)"_#Beutler. "(Beutler)"_#Beutler.
The paratemers n, alpha_LJ and alpha_C are set in the The paratemers n, alpha_LJ and alpha_C are set in the
@ -132,11 +132,34 @@ The paratemers n, alpha_LJ and alpha_C are set in the
choices for the exponent are n = 2 or n = 1. For the remaining choices for the exponent are n = 2 or n = 1. For the remaining
coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
appropriate choices. Plots of the LJ and Coulomb terms are shown appropriate choices. Plots of the LJ and Coulomb terms are shown
below, for lambda ranging from 1 ro 0 every 0.1. below, for lambda ranging from 1 to 0 every 0.1.
:c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg) :c,image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
The {lj/cut/tip4p/long/soft} implements a soft-core version of the For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
the following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
lambda (activation parameter between 0 and 1)
cutoff1 (distance units)
cutoff2 (distance units) :ul
The latter two coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style {lj/cut/soft},
since it has no Coulombic terms. For the {coul/cut/soft} and
{coul/long/soft} only lambda and the optional cutoff2 are to be
specified.
Style {lj/cut/tip4p/long/soft} implements a soft-core version of the
TIP4P water model. The usage of this pair style is documented in the TIP4P water model. The usage of this pair style is documented in the
"pair_lj"_pair_lj.html styles. The soft-core version introduces the "pair_lj"_pair_lj.html styles. The soft-core version introduces the
lambda parameter to the list of arguments, after epsilon and sigma in lambda parameter to the list of arguments, after epsilon and sigma in
@ -165,28 +188,18 @@ occur. These substyles are suitable to represent charges embedded in
the Lennard-Jones radius of another site (for example hydrogen atoms the Lennard-Jones radius of another site (for example hydrogen atoms
in several water models). in several water models).
For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, IMPORTANT NOTES: When using the core-softed Coulomb potentials with
the following coefficients must be defined for each pair of atoms long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.)
types via the "pair_coeff"_pair_coeff.html command as in the examples in a free energy calculation in which sites holding electrostatic
above, or in the data file or restart files read by the charges are being created or anihilated (using
"read_data"_read_data.html or "read_restart"_read_restart.html "fix_adapt/fep"_fix_adapt_fep.html and "compute_fep"_compute_fep.html)
commands, or by mixing as described below: it is important to adapt both the lambda activation parameter (from 0
to 1, or the reverse) and the value of the charge (from 0 to its final
epsilon (energy units) value, or the reverse). This ensures that long-range electrostatic
sigma (distance units) terms (kspace) are correct. It is not necessary to use core-softed
lambda (activation parameter between 0 and 1) Coulomb potentials if the van der Waals site is present during the
cutoff1 (distance units) free-energy route, thus avoiding overlap of the charges. Examples are
cutoff2 (distance units) :ul provided in the LAMMPS source directory tree, under examples/USER/fep.
The latter two coefficients are optional. If not specified, the global
LJ and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both LJ
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style {lj/cut/soft},
since it has no Coulombic terms. For the {coul/cut/soft} and
{coul/long/soft} only lambda and the optional cutoff2 are to be
specified.
:line :line
@ -236,9 +249,14 @@ to be specified in an input script that reads a restart file.
[Restrictions:] [Restrictions:]
To avoid division by zero do not set sigma = 0. When sites do not To avoid division by zero do not set sigma = 0; use the lambda
interact though the Lennard-Jones term use epsilon = 0 and sigma = 1 parameter instead to activate/deactivate interactions, or use
for example, or else use the {coul/long/soft} or similar substyle. epsilon = 0 and sigma = 1. Alternatively, when sites do not
interact though the Lennard-Jones term the {coul/long/soft} or
similar substyle can be used via the
"pair_style hybrid/overlay"_pair_hybrid.html command.
:line
All of the plain {soft} pair styles are part of the USER-FEP package. All of the plain {soft} pair styles are part of the USER-FEP package.
The {long} styles also requires the KSPACE package to be installed. The {long} styles also requires the KSPACE package to be installed.

44
examples/USER/fep/CH4hyd/fdti01/fdti01.lmp
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@ -1,22 +1,22 @@
# Time-averaged data for fix fFEP # Time-averaged data for fix FEP
# TimeStep c_cFEP[1] c_cFEP[2] # TimeStep c_FEP[1] c_FEP[2]
125000 0.000490778 0.999186 100000 0.000289416 0.999521
250000 0.00619786 0.989679 200000 0.00590502 0.990163
375000 0.0128045 0.978813 300000 0.0115179 0.980934
500000 0.0203102 0.96667 400000 0.0216052 0.96457
625000 0.0272161 0.955808 500000 0.0222451 0.963797
750000 0.0215735 0.965087 600000 0.0200038 0.967603
875000 0.0148509 0.975821 700000 0.0152292 0.975176
1000000 0.00936378 0.984752 800000 0.00896315 0.985384
1125000 0.00490088 0.992007 900000 0.00585213 0.990434
1250000 0.00388501 0.99366 1000000 0.00327599 0.99467
1375000 0.00122887 0.998043 1100000 0.00159845 0.997437
1500000 0.000498063 0.999247 1200000 0.000171108 0.999804
1625000 -0.000468616 1.00085 1300000 -0.000313183 1.00059
1750000 -0.00131731 1.00226 1400000 -0.00148 1.00254
1875000 -0.00247035 1.00419 1500000 -0.00297976 1.00504
2000000 -0.00306799 1.00519 1600000 -0.00287926 1.00487
2125000 -0.00355565 1.006 1700000 -0.00430671 1.00727
2250000 -0.00434289 1.00733 1800000 -0.00453729 1.00765
2375000 -0.00497634 1.00839 1900000 -0.00507356 1.00856
2500000 -0.00576373 1.00972 2000000 -0.00586954 1.0099

53
examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp
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@ -30,51 +30,54 @@ 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 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 pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
variable nsteps equal 2500000 variable TK equal 300.0
variable nprint equal ${nsteps}/500 variable PBAR equal 1.0
variable ndump equal ${nsteps}/100
variable temp equal 300.0 fix SHAKE all shake 0.0001 20 0 b 2 a 2
variable press equal 1.0
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
neighbor 2.0 bin neighbor 2.0 bin
timestep 2.0 timestep 1.0
velocity all create ${temp} 12345 velocity all create ${TK} 12345
thermo_style multi thermo_style multi
thermo ${nprint} thermo 5000
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000 fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
run 250000 set type 1*2 charge 0.0
run 100000
reset_timestep 0 reset_timestep 0
variable lambda equal ramp(0.0,1.0) variable lambda equal ramp(0.0,1.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes 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
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
variable dlambda equal 0.002 variable dlambda equal 0.002
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 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
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti01.lmp
# compute cRDF all rdf 100 3 3 3 4 4 4 dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector dump_modify TRAJ element C H O H
group owater type 3 run 2000000
compute cMSD owater msd
fix fMSD owater 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 O H
run ${nsteps}
# write_restart restart.*.lmp # write_restart restart.*.lmp
write_data data.*.lmp write_data data.*.lmp

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examples/USER/fep/CH4hyd/fdti01/log.lammps
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examples/USER/fep/CH4hyd/fdti10/fdti10.lmp
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@ -1,22 +1,22 @@
# Time-averaged data for fix fFEP # Time-averaged data for fix FEP
# TimeStep c_cFEP[1] c_cFEP[2] # TimeStep c_FEP[1] c_FEP[2]
125000 0.00652155 0.989123 100000 0.00671766 0.988799
250000 0.00572718 0.990445 200000 0.00591179 0.990139
375000 0.00506788 0.991544 300000 0.00495535 0.991733
500000 0.00448303 0.992522 400000 0.00428164 0.992859
625000 0.00370796 0.993818 500000 0.00367253 0.993879
750000 0.00277535 0.995385 600000 0.00334988 0.994424
875000 0.00230833 0.996171 700000 0.00246906 0.995908
1000000 0.000982551 0.998409 800000 0.00139088 0.997725
1125000 0.000314678 0.99954 900000 0.000491084 0.99924
1250000 -0.000839025 1.0015 1000000 0.000615407 0.999044
1375000 -0.00155615 1.00273 1100000 -0.00172714 1.00302
1500000 -0.00320598 1.00553 1200000 -0.00333962 1.00579
1625000 -0.00587133 1.01011 1300000 -0.0040424 1.00699
1750000 -0.00867306 1.01495 1400000 -0.0102385 1.01763
1875000 -0.0134768 1.02327 1500000 -0.0173611 1.03006
2000000 -0.0229314 1.03995 1600000 -0.0243837 1.04234
2125000 -0.0282333 1.04896 1700000 -0.0211518 1.03654
2250000 -0.0202762 1.03477 1800000 -0.0220119 1.03776
2375000 -0.0123279 1.02096 1900000 -0.013304 1.02261
2500000 -0.00546203 1.00923 2000000 -0.00648381 1.01095

52
examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp
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@ -30,51 +30,53 @@ 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 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 pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # H Hw
variable nsteps equal 2500000 variable TK equal 300.0
variable nprint equal ${nsteps}/500 variable PBAR equal 1.0
variable ndump equal ${nsteps}/100
variable temp equal 300.0 fix SHAKE all shake 0.0001 20 0 b 2 a 2
variable press equal 1.0
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
neighbor 2.0 bin neighbor 2.0 bin
timestep 2.0 timestep 1.0
velocity all create ${temp} 12345 velocity all create ${TK} 12345
thermo_style multi thermo_style multi
thermo ${nprint} thermo 5000
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000 fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
run 250000 run 100000
reset_timestep 0 reset_timestep 0
variable lambda equal ramp(1.0,0.0) variable lambda equal ramp(1.0,0.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes 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
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
variable dlambda equal -0.002 variable dlambda equal -0.002
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 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
fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti10.lmp
# compute cRDF all rdf 100 3 3 3 4 4 4 dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector dump_modify TRAJ element C H O H
group owater type 3 run 2000000
compute cMSD owater msd
fix fMSD owater 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 O H
run ${nsteps}
# write_restart restart.*.lmp # write_restart restart.*.lmp
write_data data.*.lmp write_data data.*.lmp

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examples/USER/fep/CH4hyd/fdti10/log.lammps
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44
examples/USER/fep/CH4hyd/fep01/fep01.lmp
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@ -1,22 +1,22 @@
# Time-averaged data for fix fFEP # Time-averaged data for fix FEP
# TimeStep c_cFEP[1] c_cFEP[2] # TimeStep c_FEP[1] c_FEP[2]
125000 0.0806308 0.881044 100000 0.0735182 0.889583
250000 0.251798 0.66945 200000 0.241868 0.679931
375000 0.448135 0.502774 300000 0.407677 0.542008
500000 0.670275 0.384034 400000 0.709112 0.360902
625000 0.873864 0.343148 500000 0.718538 0.428553
750000 0.689533 0.484145 600000 0.639674 0.516854
875000 0.474153 0.600305 700000 0.482835 0.586307
1000000 0.303566 0.740249 800000 0.289216 0.746055
1125000 0.165693 0.855143 900000 0.192641 0.823932
1250000 0.130949 0.88524 1000000 0.113029 0.908737
1375000 0.0518948 0.976114 1100000 0.0619301 0.96572
1500000 0.0283335 1.0025 1200000 0.0197356 1.01976
1625000 -0.000790228 1.04259 1300000 0.00310596 1.03223
1750000 -0.0263791 1.0736 1400000 -0.0300484 1.08295
1875000 -0.0587947 1.12568 1500000 -0.0714914 1.14599
2000000 -0.0764999 1.15472 1600000 -0.0712604 1.14573
2125000 -0.091264 1.17869 1700000 -0.109089 1.2123
2250000 -0.11294 1.21778 1800000 -0.117256 1.22671
2375000 -0.130721 1.25162 1900000 -0.132337 1.25534
2500000 -0.151808 1.29392 2000000 -0.153557 1.29745

53
examples/USER/fep/CH4hyd/fep01/in.fep01.lmp
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@ -30,51 +30,54 @@ 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 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 pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
variable nsteps equal 2500000 variable TK equal 300.0
variable nprint equal ${nsteps}/500 variable PBAR equal 1.0
variable ndump equal ${nsteps}/100
variable temp equal 300.0 fix SHAKE all shake 0.0001 20 0 b 2 a 2
variable press equal 1.0
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
neighbor 2.0 bin neighbor 2.0 bin
timestep 2.0 timestep 1.0
velocity all create ${temp} 12345 velocity all create ${TK} 12345
thermo_style multi thermo_style multi
thermo ${nprint} thermo 5000
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000 fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
run 250000 set type 1*2 charge 0.0
run 100000
reset_timestep 0 reset_timestep 0
variable lambda equal ramp(0.0,1.0) variable lambda equal ramp(0.0,1.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes 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
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
variable dlambda equal 0.05 variable dlambda equal 0.05
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 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
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[1] c_FEP[2] file fep01.lmp
# compute cRDF all rdf 100 3 3 3 4 4 4 dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector dump_modify TRAJ element C H O H
group owater type 3 run 2000000
compute cMSD owater msd
fix fMSD owater 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 O H
run ${nsteps}
# write_restart restart.*.lmp # write_restart restart.*.lmp
write_data data.*.lmp write_data data.*.lmp

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examples/USER/fep/CH4hyd/fep01/log.lammps
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44
examples/USER/fep/CH4hyd/fep10/fep10.lmp
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@ -1,22 +1,22 @@
# Time-averaged data for fix fFEP # Time-averaged data for fix FEP
# TimeStep c_cFEP[1] c_cFEP[2] # TimeStep c_FEP[1] c_FEP[2]
125000 0.156203 0.771285 100000 0.160455 0.766272
250000 0.136448 0.799233 200000 0.141912 0.791902
375000 0.12198 0.820426 300000 0.119585 0.824744
500000 0.109453 0.840255 400000 0.104694 0.847809
625000 0.0921141 0.868102 500000 0.0917124 0.869318
750000 0.0713015 0.905735 600000 0.0859541 0.881974
875000 0.0622431 0.922352 700000 0.0666319 0.920268
1000000 0.0330546 0.981942 800000 0.0428654 0.965893
1125000 0.0197866 1.01134 900000 0.0240106 0.999889
1250000 -0.00412826 1.06765 1000000 0.0294147 0.997671
1375000 -0.0174302 1.11343 1100000 -0.0214947 1.11583
1500000 -0.0511646 1.18453 1200000 -0.0543642 1.23078
1625000 -0.105676 1.36325 1300000 -0.0665772 1.25986
1750000 -0.161616 1.56478 1400000 -0.196675 1.66521
1875000 -0.258263 1.93825 1500000 -0.341037 2.39926
2000000 -0.447487 3.0595 1600000 -0.480217 2.97287
2125000 -0.549377 3.01163 1700000 -0.405599 2.36311
2250000 -0.379009 2.01933 1800000 -0.415165 2.12414
2375000 -0.20934 1.45678 1900000 -0.229669 1.49644
2500000 -0.0644056 1.1252 2000000 -0.0838847 1.15743

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examples/USER/fep/CH4hyd/fep10/in.fep10.lmp
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@ -30,51 +30,53 @@ 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 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 pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # H Hw
variable nsteps equal 2500000 variable TK equal 300.0
variable nprint equal ${nsteps}/500 variable PBAR equal 1.0
variable ndump equal ${nsteps}/100
variable temp equal 300.0 fix SHAKE all shake 0.0001 20 0 b 2 a 2
variable press equal 1.0
fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
neighbor 2.0 bin neighbor 2.0 bin
timestep 2.0 timestep 1.0
velocity all create ${temp} 12345 velocity all create ${TK} 12345
thermo_style multi thermo_style multi
thermo ${nprint} thermo 5000
fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000 fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
run 250000 run 100000
reset_timestep 0 reset_timestep 0
variable lambda equal ramp(1.0,0.0) variable lambda equal ramp(1.0,0.0)
variable q1 equal -0.24*v_lambda
variable q2 equal 0.06*v_lambda
fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes 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
fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
variable dlambda equal -0.05 variable dlambda equal -0.05
variable dq1 equal -0.24*v_dlambda
variable dq2 equal 0.06*v_dlambda
compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 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
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[1] c_FEP[2] file fep10.lmp
# compute cRDF all rdf 100 3 3 3 4 4 4 dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector dump_modify TRAJ element C H O H
group owater type 3 run 2000000
compute cMSD owater msd
fix fMSD owater 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 O H
run ${nsteps}
# write_restart restart.*.lmp # write_restart restart.*.lmp
write_data data.*.lmp write_data data.*.lmp

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examples/USER/fep/CH4hyd/fep10/log.lammps
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