Commit c3fd4101 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13464 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 2284dcc4

examples/USER/fep/CH4hyd/fdti01/fdti01.lmp

+22 −22
Original line number Diff line number Diff line 
# Time-averaged data for fix fFEP

# TimeStep c_cFEP[1] c_cFEP[2]

125000 0.000490778 0.999186

250000 0.00619786 0.989679

375000 0.0128045 0.978813

500000 0.0203102 0.96667

625000 0.0272161 0.955808

750000 0.0215735 0.965087

875000 0.0148509 0.975821

1000000 0.00936378 0.984752

1125000 0.00490088 0.992007

1250000 0.00388501 0.99366

1375000 0.00122887 0.998043

1500000 0.000498063 0.999247

1625000 -0.000468616 1.00085

1750000 -0.00131731 1.00226

1875000 -0.00247035 1.00419

2000000 -0.00306799 1.00519

2125000 -0.00355565 1.006

2250000 -0.00434289 1.00733

2375000 -0.00497634 1.00839

2500000 -0.00576373 1.00972
 
# 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

examples/USER/fep/CH4hyd/fdti01/in.fdti01.lmp

+28 −25
Original line number Diff line number Diff line
@@ -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    4  lj/cut/tip4p/long/soft   0.0000   1.0000  0.0  # H Hw



variable nsteps equal 2500000

variable nprint equal ${nsteps}/500

variable ndump equal ${nsteps}/100

variable TK equal 300.0

variable PBAR equal 1.0



variable temp equal 300.0

variable press equal 1.0



fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2

fix SHAKE all shake 0.0001 20 0 b 2 a 2



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}

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



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



variable dlambda equal 0.002

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



compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda

fix PRINT all print 100000 "adapt  lambda = ${lambda}  q1 = ${q1}  q2 = ${q2}"

  

fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp

variable dlambda equal 0.002

variable dq1 equal -0.24*v_dlambda

variable dq2 equal  0.06*v_dlambda



# compute cRDF all rdf 100 3 3 3 4 4 4

# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector

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



group owater type 3

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

fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti01.lmp



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

dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz

dump_modify TRAJ element C H O H



run ${nsteps}

run 2000000



# write_restart restart.*.lmp

write_data data.*.lmp

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

+2631 −5051

File changed.

Preview size limit exceeded, changes collapsed.

examples/USER/fep/CH4hyd/fdti10/fdti10.lmp

+22 −22
Original line number Diff line number Diff line 
# Time-averaged data for fix fFEP

# TimeStep c_cFEP[1] c_cFEP[2]

125000 0.00652155 0.989123

250000 0.00572718 0.990445

375000 0.00506788 0.991544

500000 0.00448303 0.992522

625000 0.00370796 0.993818

750000 0.00277535 0.995385

875000 0.00230833 0.996171

1000000 0.000982551 0.998409

1125000 0.000314678 0.99954

1250000 -0.000839025 1.0015

1375000 -0.00155615 1.00273

1500000 -0.00320598 1.00553

1625000 -0.00587133 1.01011

1750000 -0.00867306 1.01495

1875000 -0.0134768 1.02327

2000000 -0.0229314 1.03995

2125000 -0.0282333 1.04896

2250000 -0.0202762 1.03477

2375000 -0.0123279 1.02096

2500000 -0.00546203 1.00923
 
# 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

examples/USER/fep/CH4hyd/fdti10/in.fdti10.lmp

+27 −25
Original line number Diff line number Diff line
@@ -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    4  lj/cut/tip4p/long/soft   0.0000   1.0000  1.0  # H Hw



variable nsteps equal 2500000

variable nprint equal ${nsteps}/500

variable ndump equal ${nsteps}/100

variable TK equal 300.0

variable PBAR equal 1.0



variable temp equal 300.0

variable press equal 1.0



fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2

fix SHAKE all shake 0.0001 20 0 b 2 a 2



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}

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



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



variable dlambda equal -0.002

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



compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda

fix PRINT all print 100000 "adapt  lambda = ${lambda}  q1 = ${q1}  q2 = ${q2}"

  

fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp

variable dlambda equal -0.002

variable dq1 equal -0.24*v_dlambda

variable dq2 equal  0.06*v_dlambda



# compute cRDF all rdf 100 3 3 3 4 4 4

# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector

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



group owater type 3

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

fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti10.lmp



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

dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz

dump_modify TRAJ element C H O H



run ${nsteps}

run 2000000



# write_restart restart.*.lmp

write_data data.*.lmp

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