mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13464 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
2284dcc452
commit
c3fd41010d
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@ -1,22 +1,22 @@
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# Time-averaged data for fix fFEP
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# TimeStep c_cFEP[1] c_cFEP[2]
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125000 0.000490778 0.999186
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250000 0.00619786 0.989679
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375000 0.0128045 0.978813
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500000 0.0203102 0.96667
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625000 0.0272161 0.955808
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750000 0.0215735 0.965087
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875000 0.0148509 0.975821
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1000000 0.00936378 0.984752
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1125000 0.00490088 0.992007
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1250000 0.00388501 0.99366
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1375000 0.00122887 0.998043
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1500000 0.000498063 0.999247
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1625000 -0.000468616 1.00085
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1750000 -0.00131731 1.00226
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1875000 -0.00247035 1.00419
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2000000 -0.00306799 1.00519
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2125000 -0.00355565 1.006
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2250000 -0.00434289 1.00733
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2375000 -0.00497634 1.00839
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2500000 -0.00576373 1.00972
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# Time-averaged data for fix FEP
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# TimeStep c_FEP[1] c_FEP[2]
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100000 0.000289416 0.999521
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200000 0.00590502 0.990163
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300000 0.0115179 0.980934
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400000 0.0216052 0.96457
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500000 0.0222451 0.963797
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600000 0.0200038 0.967603
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700000 0.0152292 0.975176
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800000 0.00896315 0.985384
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900000 0.00585213 0.990434
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1000000 0.00327599 0.99467
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1100000 0.00159845 0.997437
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1200000 0.000171108 0.999804
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1300000 -0.000313183 1.00059
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1400000 -0.00148 1.00254
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1500000 -0.00297976 1.00504
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1600000 -0.00287926 1.00487
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1700000 -0.00430671 1.00727
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1800000 -0.00453729 1.00765
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1900000 -0.00507356 1.00856
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2000000 -0.00586954 1.0099
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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
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pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
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pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
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variable nsteps equal 2500000
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variable nprint equal ${nsteps}/500
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variable ndump equal ${nsteps}/100
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variable TK equal 300.0
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variable PBAR equal 1.0
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variable temp equal 300.0
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variable press equal 1.0
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fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
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fix SHAKE all shake 0.0001 20 0 b 2 a 2
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neighbor 2.0 bin
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timestep 2.0
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timestep 1.0
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velocity all create ${temp} 12345
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velocity all create ${TK} 12345
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thermo_style multi
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thermo ${nprint}
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thermo 5000
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fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
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fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
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run 250000
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set type 1*2 charge 0.0
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run 100000
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reset_timestep 0
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variable lambda equal ramp(0.0,1.0)
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variable q1 equal -0.24*v_lambda
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variable q2 equal 0.06*v_lambda
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fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
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fix ADAPT all adapt/fep 100000 &
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pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda &
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atom charge 1 v_q1 &
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atom charge 2 v_q2 &
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after yes
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fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
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variable dlambda equal 0.002
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variable dq1 equal -0.24*v_dlambda
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variable dq2 equal 0.06*v_dlambda
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compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
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compute FEP all fep ${TK} &
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pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
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atom charge 1 v_dq1 &
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atom charge 2 v_dq2
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fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti01.lmp
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fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti01.lmp
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# compute cRDF all rdf 100 3 3 3 4 4 4
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# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
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dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify TRAJ element C H O H
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group owater type 3
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compute cMSD owater msd
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fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
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dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify dCONF element C H O H
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run ${nsteps}
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run 2000000
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# write_restart restart.*.lmp
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write_data data.*.lmp
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File diff suppressed because it is too large
Load Diff
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@ -1,22 +1,22 @@
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# Time-averaged data for fix fFEP
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# TimeStep c_cFEP[1] c_cFEP[2]
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125000 0.00652155 0.989123
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250000 0.00572718 0.990445
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375000 0.00506788 0.991544
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500000 0.00448303 0.992522
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625000 0.00370796 0.993818
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750000 0.00277535 0.995385
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875000 0.00230833 0.996171
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1000000 0.000982551 0.998409
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1125000 0.000314678 0.99954
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1250000 -0.000839025 1.0015
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1375000 -0.00155615 1.00273
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1500000 -0.00320598 1.00553
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1625000 -0.00587133 1.01011
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1750000 -0.00867306 1.01495
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1875000 -0.0134768 1.02327
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2000000 -0.0229314 1.03995
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2125000 -0.0282333 1.04896
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2250000 -0.0202762 1.03477
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2375000 -0.0123279 1.02096
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2500000 -0.00546203 1.00923
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# Time-averaged data for fix FEP
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# TimeStep c_FEP[1] c_FEP[2]
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100000 0.00671766 0.988799
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200000 0.00591179 0.990139
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300000 0.00495535 0.991733
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400000 0.00428164 0.992859
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500000 0.00367253 0.993879
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600000 0.00334988 0.994424
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700000 0.00246906 0.995908
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800000 0.00139088 0.997725
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900000 0.000491084 0.99924
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1000000 0.000615407 0.999044
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1100000 -0.00172714 1.00302
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1200000 -0.00333962 1.00579
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1300000 -0.0040424 1.00699
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1400000 -0.0102385 1.01763
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1500000 -0.0173611 1.03006
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1600000 -0.0243837 1.04234
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1700000 -0.0211518 1.03654
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1800000 -0.0220119 1.03776
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1900000 -0.013304 1.02261
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2000000 -0.00648381 1.01095
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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
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pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 1.0 # H Ow
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pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 1.0 # H Hw
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variable nsteps equal 2500000
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variable nprint equal ${nsteps}/500
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variable ndump equal ${nsteps}/100
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variable TK equal 300.0
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variable PBAR equal 1.0
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variable temp equal 300.0
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variable press equal 1.0
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|
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fix fSHAKE all shake 0.0001 20 ${nprint} b 2 a 2
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fix SHAKE all shake 0.0001 20 0 b 2 a 2
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neighbor 2.0 bin
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timestep 2.0
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timestep 1.0
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velocity all create ${temp} 12345
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velocity all create ${TK} 12345
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thermo_style multi
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thermo ${nprint}
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thermo 5000
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|
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fix fNPT all npt temp ${temp} ${temp} 100 iso ${press} ${press} 1000
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fix TPSTAT all npt temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 1000
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run 250000
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run 100000
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reset_timestep 0
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variable lambda equal ramp(1.0,0.0)
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variable q1 equal -0.24*v_lambda
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variable q2 equal 0.06*v_lambda
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|
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fix fADAPT all adapt/fep 125000 pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda after yes
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fix ADAPT all adapt/fep 100000 &
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pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_lambda &
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atom charge 1 v_q1 &
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atom charge 2 v_q2 &
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after yes
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fix PRINT all print 100000 "adapt lambda = ${lambda} q1 = ${q1} q2 = ${q2}"
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variable dlambda equal -0.002
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variable dq1 equal -0.24*v_dlambda
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variable dq2 equal 0.06*v_dlambda
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compute cFEP all fep ${temp} pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda
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compute FEP all fep ${TK} &
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pair lj/cut/tip4p/long/soft lambda 1*2 3*4 v_dlambda &
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atom charge 1 v_dq1 &
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atom charge 2 v_dq2
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fix fFEP all ave/time 25 4000 125000 c_cFEP[1] c_cFEP[2] file fdti10.lmp
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fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fdti10.lmp
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# compute cRDF all rdf 100 3 3 3 4 4 4
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# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
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dump TRAJ all custom 20000 dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify TRAJ element C H O H
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group owater type 3
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compute cMSD owater msd
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fix fMSD owater ave/time 1 1 ${ndump} c_cMSD[1] c_cMSD[2] c_cMSD[3] c_cMSD[4] file msd.lammps
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dump dCONF all custom ${ndump} dump.lammpstrj id mol type element x y z ix iy iz
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dump_modify dCONF element C H O H
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run ${nsteps}
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run 2000000
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# write_restart restart.*.lmp
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write_data data.*.lmp
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|
|
|
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File diff suppressed because it is too large
Load Diff
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@ -1,22 +1,22 @@
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# Time-averaged data for fix fFEP
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# TimeStep c_cFEP[1] c_cFEP[2]
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125000 0.0806308 0.881044
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250000 0.251798 0.66945
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375000 0.448135 0.502774
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500000 0.670275 0.384034
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625000 0.873864 0.343148
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750000 0.689533 0.484145
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875000 0.474153 0.600305
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1000000 0.303566 0.740249
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1125000 0.165693 0.855143
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1250000 0.130949 0.88524
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1375000 0.0518948 0.976114
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1500000 0.0283335 1.0025
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1625000 -0.000790228 1.04259
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1750000 -0.0263791 1.0736
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1875000 -0.0587947 1.12568
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2000000 -0.0764999 1.15472
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2125000 -0.091264 1.17869
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2250000 -0.11294 1.21778
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2375000 -0.130721 1.25162
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2500000 -0.151808 1.29392
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# Time-averaged data for fix FEP
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# TimeStep c_FEP[1] c_FEP[2]
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100000 0.0735182 0.889583
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200000 0.241868 0.679931
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300000 0.407677 0.542008
|
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400000 0.709112 0.360902
|
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500000 0.718538 0.428553
|
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600000 0.639674 0.516854
|
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700000 0.482835 0.586307
|
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800000 0.289216 0.746055
|
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900000 0.192641 0.823932
|
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1000000 0.113029 0.908737
|
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1100000 0.0619301 0.96572
|
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1200000 0.0197356 1.01976
|
||||
1300000 0.00310596 1.03223
|
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1400000 -0.0300484 1.08295
|
||||
1500000 -0.0714914 1.14599
|
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1600000 -0.0712604 1.14573
|
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1700000 -0.109089 1.2123
|
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1800000 -0.117256 1.22671
|
||||
1900000 -0.132337 1.25534
|
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2000000 -0.153557 1.29745
|
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|
|
|
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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
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|||
pair_coeff 2 3 lj/cut/tip4p/long/soft 0.0699 2.8126 0.0 # H Ow
|
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pair_coeff 2 4 lj/cut/tip4p/long/soft 0.0000 1.0000 0.0 # H Hw
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||||
|
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variable nsteps equal 2500000
|
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variable nprint equal ${nsteps}/500
|
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variable ndump equal ${nsteps}/100
|
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variable TK equal 300.0
|
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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
|
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fix SHAKE all shake 0.0001 20 0 b 2 a 2
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|
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neighbor 2.0 bin
|
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|
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timestep 2.0
|
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timestep 1.0
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|
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velocity all create ${temp} 12345
|
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velocity all create ${TK} 12345
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|
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thermo_style multi
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thermo ${nprint}
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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
|
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|
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run 250000
|
||||
set type 1*2 charge 0.0
|
||||
|
||||
run 100000
|
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reset_timestep 0
|
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|
||||
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 &
|
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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 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
|
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fix FEP all ave/time 20 4000 100000 c_FEP[1] c_FEP[2] file fep01.lmp
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||||
|
||||
# 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
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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}
|
||||
run 2000000
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -1,22 +1,22 @@
|
|||
# Time-averaged data for fix fFEP
|
||||
# TimeStep c_cFEP[1] c_cFEP[2]
|
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125000 0.156203 0.771285
|
||||
250000 0.136448 0.799233
|
||||
375000 0.12198 0.820426
|
||||
500000 0.109453 0.840255
|
||||
625000 0.0921141 0.868102
|
||||
750000 0.0713015 0.905735
|
||||
875000 0.0622431 0.922352
|
||||
1000000 0.0330546 0.981942
|
||||
1125000 0.0197866 1.01134
|
||||
1250000 -0.00412826 1.06765
|
||||
1375000 -0.0174302 1.11343
|
||||
1500000 -0.0511646 1.18453
|
||||
1625000 -0.105676 1.36325
|
||||
1750000 -0.161616 1.56478
|
||||
1875000 -0.258263 1.93825
|
||||
2000000 -0.447487 3.0595
|
||||
2125000 -0.549377 3.01163
|
||||
2250000 -0.379009 2.01933
|
||||
2375000 -0.20934 1.45678
|
||||
2500000 -0.0644056 1.1252
|
||||
# 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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
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 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
|
||||
# fix fRDF all ave/time 2000 500 ${nsteps} c_cRDF file rdf.lammps mode vector
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
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}
|
||||
run 2000000
|
||||
|
||||
# write_restart restart.*.lmp
|
||||
write_data data.*.lmp
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -81,7 +81,7 @@ __kernel void k_coul_dsf(const __global numtyp4 *restrict x_,
|
|||
int j=dev_packed[nbor];
|
||||
|
||||
numtyp factor_coul, r, prefactor, erfcc;
|
||||
factor_coul = sp_lj[sbmask(j)];
|
||||
factor_coul = (numtyp)1.0-sp_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
||||
|
|
@ -98,12 +98,12 @@ __kernel void k_coul_dsf(const __global numtyp4 *restrict x_,
|
|||
|
||||
r = ucl_sqrt(rsq);
|
||||
fetch(prefactor,j,q_tex);
|
||||
prefactor *= factor_coul * qqrd2e*qtmp/r;
|
||||
prefactor *= qqrd2e*qtmp/r;
|
||||
numtyp erfcd = ucl_exp(-alpha*alpha*rsq);
|
||||
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc + (numtyp)2.0*alpha/MY_PIS*r*erfcd +
|
||||
rsq*f_shift);
|
||||
rsq*f_shift-factor_coul);
|
||||
|
||||
force = forcecoul * r2inv;
|
||||
|
||||
|
|
@ -112,10 +112,8 @@ __kernel void k_coul_dsf(const __global numtyp4 *restrict x_,
|
|||
f.z+=delz*force;
|
||||
|
||||
if (eflag>0) {
|
||||
if (rsq < cut_coulsq) {
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift);
|
||||
e_coul += e;
|
||||
}
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift-factor_coul);
|
||||
e_coul += e;
|
||||
}
|
||||
if (vflag>0) {
|
||||
virial[0] += delx*delx*force;
|
||||
|
|
@ -182,7 +180,7 @@ __kernel void k_coul_dsf_fast(const __global numtyp4 *restrict x_,
|
|||
int j=dev_packed[nbor];
|
||||
|
||||
numtyp factor_coul, r, prefactor, erfcc;
|
||||
factor_coul = sp_lj[sbmask(j)];
|
||||
factor_coul = (numtyp)1.0-sp_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
||||
|
|
@ -199,12 +197,12 @@ __kernel void k_coul_dsf_fast(const __global numtyp4 *restrict x_,
|
|||
|
||||
r = ucl_sqrt(rsq);
|
||||
fetch(prefactor,j,q_tex);
|
||||
prefactor *= factor_coul * qqrd2e*qtmp/r;
|
||||
prefactor *= qqrd2e*qtmp/r;
|
||||
numtyp erfcd = ucl_exp(-alpha*alpha*rsq);
|
||||
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc + (numtyp)2.0*alpha/MY_PIS*r*erfcd +
|
||||
rsq*f_shift);
|
||||
rsq*f_shift-factor_coul);
|
||||
|
||||
force = forcecoul * r2inv;
|
||||
|
||||
|
|
@ -213,10 +211,8 @@ __kernel void k_coul_dsf_fast(const __global numtyp4 *restrict x_,
|
|||
f.z+=delz*force;
|
||||
|
||||
if (eflag>0) {
|
||||
if (rsq < cut_coulsq) {
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift);
|
||||
e_coul += e;
|
||||
}
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift-factor_coul);
|
||||
e_coul += e;
|
||||
}
|
||||
if (vflag>0) {
|
||||
virial[0] += delx*delx*force;
|
||||
|
|
|
|||
|
|
@ -89,7 +89,7 @@ __kernel void k_lj_dsf(const __global numtyp4 *restrict x_,
|
|||
|
||||
numtyp factor_lj, factor_coul, r, prefactor, erfcc;
|
||||
factor_lj = sp_lj[sbmask(j)];
|
||||
factor_coul = sp_lj[sbmask(j)+4];
|
||||
factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
||||
|
|
@ -115,12 +115,12 @@ __kernel void k_lj_dsf(const __global numtyp4 *restrict x_,
|
|||
if (rsq < cut_coulsq) {
|
||||
r = ucl_sqrt(rsq);
|
||||
fetch(prefactor,j,q_tex);
|
||||
prefactor *= factor_coul * qqrd2e*qtmp/r;
|
||||
prefactor *= qqrd2e*qtmp/r;
|
||||
numtyp erfcd = ucl_exp(-alpha*alpha*rsq);
|
||||
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc + (numtyp)2.0*alpha/MY_PIS*r*erfcd +
|
||||
rsq*f_shift);
|
||||
rsq*f_shift-factor_coul);
|
||||
} else
|
||||
forcecoul = (numtyp)0.0;
|
||||
|
||||
|
|
@ -132,7 +132,7 @@ __kernel void k_lj_dsf(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (eflag>0) {
|
||||
if (rsq < cut_coulsq) {
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift);
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift-factor_coul);
|
||||
e_coul += e;
|
||||
}
|
||||
if (rsq < lj1[mtype].z) {
|
||||
|
|
@ -217,7 +217,7 @@ __kernel void k_lj_dsf_fast(const __global numtyp4 *restrict x_,
|
|||
|
||||
numtyp factor_lj, factor_coul, r, prefactor, erfcc;
|
||||
factor_lj = sp_lj[sbmask(j)];
|
||||
factor_coul = sp_lj[sbmask(j)+4];
|
||||
factor_coul = (numtyp)1.0-sp_lj[sbmask(j)+4];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
|
||||
|
|
@ -242,12 +242,12 @@ __kernel void k_lj_dsf_fast(const __global numtyp4 *restrict x_,
|
|||
if (rsq < cut_coulsq) {
|
||||
r = ucl_sqrt(rsq);
|
||||
fetch(prefactor,j,q_tex);
|
||||
prefactor *= factor_coul * qqrd2e*qtmp/r;
|
||||
prefactor *= qqrd2e*qtmp/r;
|
||||
numtyp erfcd = ucl_exp(-alpha*alpha*rsq);
|
||||
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc + (numtyp)2.0*alpha/MY_PIS*r*erfcd +
|
||||
rsq*f_shift);
|
||||
rsq*f_shift-factor_coul);
|
||||
} else
|
||||
forcecoul = (numtyp)0.0;
|
||||
|
||||
|
|
@ -259,7 +259,7 @@ __kernel void k_lj_dsf_fast(const __global numtyp4 *restrict x_,
|
|||
|
||||
if (eflag>0) {
|
||||
if (rsq < cut_coulsq) {
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift);
|
||||
numtyp e=prefactor*(erfcc-r*e_shift-rsq*f_shift-factor_coul);
|
||||
e_coul += e;
|
||||
}
|
||||
if (rsq < lj1[mtype].z) {
|
||||
|
|
|
|||
|
|
@ -203,7 +203,7 @@ void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
int i,j,ii,jj,jnum;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
|
||||
double r,rsq,r2inv,forcecoul,factor_coul;
|
||||
double prefactor,erfcc,erfcd,e_self,t;
|
||||
double prefactor,erfcc,erfcd,t;
|
||||
int *jlist;
|
||||
|
||||
ecoul = 0.0;
|
||||
|
|
@ -227,7 +227,7 @@ void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
jnum = numneigh[i];
|
||||
|
||||
if (evflag) {
|
||||
e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
}
|
||||
|
||||
|
|
@ -244,13 +244,14 @@ void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
if (rsq < cut_coulsq) {
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
erfcd = exp(-alpha*alpha*r*r);
|
||||
t = 1.0 / (1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
|
||||
fpair = forcecoul * r2inv;
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
|
|
@ -259,6 +260,7 @@ void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -205,7 +205,7 @@ void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
int i,j,ii,jj,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double r,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||
double prefactor,erfcc,erfcd,e_self,t;
|
||||
double prefactor,erfcc,erfcd,t;
|
||||
int *jlist;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
|
|
@ -232,7 +232,7 @@ void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
jnum = numneigh[i];
|
||||
|
||||
if (evflag) {
|
||||
e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
}
|
||||
|
||||
|
|
@ -258,12 +258,13 @@ void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
erfcd = exp(-alpha*alpha*r*r);
|
||||
t = 1.0 / (1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
|
||||
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
|
@ -280,6 +281,7 @@ void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag,
|
|||
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -125,7 +125,7 @@ void PairBornCoulWolfOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
|
||||
qisq = qtmp*qtmp;
|
||||
e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
|
||||
if (EVFLAG) ev_tally_thr(this,i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0,thr);
|
||||
if (EFLAG) ev_tally_thr(this,i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0,thr);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
|
|
|
|||
|
|
@ -138,14 +138,14 @@ void PairCoulDSFOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
r2inv = 1.0/rsq;
|
||||
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
erfcd = exp(-alpha*alpha*rsq);
|
||||
t = 1.0 / (1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
fpair = forcecoul * r2inv;
|
||||
if (EFLAG) ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
|
|
@ -156,6 +156,11 @@ void PairCoulDSFOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
f[j].z -= delz*fpair;
|
||||
}
|
||||
|
||||
if (EFLAG) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
|
||||
0.0,ecoul,fpair,delx,dely,delz,thr);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -122,7 +122,7 @@ void PairLJCutCoulDSFOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
jnum = numneigh[i];
|
||||
fxtmp=fytmp=fztmp=0.0;
|
||||
|
||||
if (EVFLAG) {
|
||||
if (EFLAG) {
|
||||
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
ev_tally_thr(this,i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0,thr);
|
||||
}
|
||||
|
|
@ -145,19 +145,21 @@ void PairLJCutCoulDSFOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
forcelj *= factor_lj;
|
||||
} else forcelj = 0.0;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
erfcd = exp(-alpha*alpha*r*r);
|
||||
t = 1.0 / (1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
fpair = forcecoul * r2inv;
|
||||
} else forcecoul = 0.0;
|
||||
fpair = (forcecoul + forcelj) * r2inv;
|
||||
|
||||
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
||||
fxtmp += delx*fpair;
|
||||
fytmp += dely*fpair;
|
||||
|
|
@ -171,12 +173,13 @@ void PairLJCutCoulDSFOMP::eval(int iifrom, int iito, ThrData * const thr)
|
|||
if (EFLAG) {
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
|
||||
offset[itype][jtype];
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -115,7 +115,7 @@ void PairBornCoulWolf::compute(int eflag, int vflag)
|
|||
|
||||
qisq = qtmp*qtmp;
|
||||
e_self = -(e_shift/2.0 + alf/MY_PIS) * qisq*qqrd2e;
|
||||
if (evflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
if (eflag) ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
|
|
|
|||
|
|
@ -67,7 +67,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
|
|||
int i,j,ii,jj,inum,jnum;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
|
||||
double r,rsq,r2inv,forcecoul,factor_coul;
|
||||
double prefactor,erfcc,erfcd,e_self,t;
|
||||
double prefactor,erfcc,erfcd,t;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
ecoul = 0.0;
|
||||
|
|
@ -99,7 +99,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
|
|||
jnum = numneigh[i];
|
||||
|
||||
if (eflag) {
|
||||
e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
double e_self = -(e_shift/2.0 + alpha/MY_PIS) * qtmp*qtmp*qqrd2e;
|
||||
ev_tally(i,i,nlocal,0,0.0,e_self,0.0,0.0,0.0,0.0);
|
||||
}
|
||||
|
||||
|
|
@ -117,14 +117,15 @@ void PairCoulDSF::compute(int eflag, int vflag)
|
|||
r2inv = 1.0/rsq;
|
||||
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
erfcd = exp(-alpha*alpha*rsq);
|
||||
t = 1.0 / (1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
fpair = forcecoul * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
|
|
@ -136,6 +137,7 @@ void PairCoulDSF::compute(int eflag, int vflag)
|
|||
|
||||
if (eflag) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
|
|
|
|||
|
|
@ -133,11 +133,9 @@ void PairCoulWolf::compute(int eflag, int vflag)
|
|||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = v_sh;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
}
|
||||
ecoul = v_sh;
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
0.0,ecoul,fpair,delx,dely,delz);
|
||||
|
|
|
|||
|
|
@ -138,12 +138,14 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
|
|||
|
||||
if (rsq < cut_coulsq) {
|
||||
r = sqrt(rsq);
|
||||
prefactor = factor_coul * qqrd2e*qtmp*q[j]/r;
|
||||
prefactor = qqrd2e*qtmp*q[j]/r;
|
||||
erfcd = exp(-alpha*alpha*r*r);
|
||||
t = 1.0 / (1.0 + EWALD_P*alpha*r);
|
||||
erfcc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * erfcd;
|
||||
forcecoul = prefactor * (erfcc/r + 2.0*alpha/MY_PIS * erfcd +
|
||||
r*f_shift) * r;
|
||||
r*f_shift) * r;
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
fpair = forcecoul * r2inv;
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
|
||||
|
|
@ -162,9 +164,10 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag)
|
|||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
ecoul = prefactor * (erfcc - r*e_shift - rsq*f_shift);
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue