git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7062 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/README

@@ -29,6 +29,7 @@ colloid:  big colloid particles in a small particle solvent, 2d system
 comb:	  models using the COMB potential
 crack:	  crack propagation in a 2d solid
 dipole:   point dipolar particles, 2d system
+dreiding: methanol via Dreiding FF
 eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
 flow:	  Couette and Poiseuille flow in a 2d channel

examples/dreiding/README

+The LAMMPS input script and data file were built to
+match the Cerius Dreiding files included
+in this directory (ch3oh.box.*) so that you
+can compare LAMMPS output to a Dreiding implementation
+in the Cerius code.

examples/dreiding/ch3oh.box.dreiding.cerius2.eng.dat

+Energy expression created for 3D-periodic boundary conditions.
+  Cell information:
+    Density (g/cc):      0.4573
+    Volume  (A**3):   7447.2363
+          A:     19.9969          Alpha:     90.0000
+          B:     19.1282          Beta :     90.0000
+          C:     19.4697          Gamma:     90.0000
+
+  Summary of the energy expression:
+  Movable atoms          :    384     Fixed atoms            :      0
+  Polar atoms            :      0
+  Bonds                  :    320     Angles                 :    448
+  Torsions               :    192     Inversions             :      0
+  Urey-Bradley           :      0     Bend-bend              :      0
+  Stretch-stretch        :      0     Sep-stretch-stretch    :      0
+  Stretch-bend-stretch   :      0     Torsion-stretch        :      0
+  Torsion-bend-bend      :      0     Stretch-torsion-stretch:      0
+  Bend-torsion-bend      :      0
+  Hydrogen-bond acceptors:     64     Hydrogen-bond donors   :     64
+  Nonbond exclusions     :    768     Polar-polar exclusions :      0
+
+  Total charge           :     -0.001 Movable atoms only     :     -0.001
+  Total mass             :   2050.688 Movable atoms only     :   2050.688
+
+Automatically calculating Ewald parameters for Coulomb sum.
+
+Summary of Non-bond set up :- 
+    Non-bond list cutoff radius     :  13.530 (A) 
+    Number of non-bond terms in list : 101788 
+    This has been updated 1 times since the energy expression was created.
+
+  Using Ewald sums for Coulomb terms with: 
+   Eta=3.932,  Rcut=11.530, Kcut=0.298,  Acc.=0.001
+
+VDW terms truncated at : 8.500 (A)
+
+Diagonal VdW parameters combined using the arithmetic combination rule.
+
+Summary of H-bond set up using a h-bond list.
+
+There are 604 interactions within hbond cutoffs of 
+  Donor-acceptor distances less than 6.500 (A) and 
+  Donor-h-acceptor angles greater than 90.000 (degrees) 
+
+************************************************************************
+                        Energy Decomposition
+             Valence Terms                         Nonbond Terms
+  Bonds         :  0.535675            Van der Waals :  -56.0592
+  Angles        :   1.28188            Electrostatic :   234.036
+  Torsions      :   1.23250            Hydrogen Bonds:  -68.7337
+  Inversions    :  0.000000E+00        Restraints    :  0.000000E+00
+  Urey-Bradley  :  0.000000E+00        3-Body        :  0.000000E+00
+  Cross-Terms   :  0.000000E+00
+  Total Energy  :   112.293
+************************************************************************
+

examples/dreiding/in.dreiding

+units           real
+atom_style      full
+boundary        p p p
+dielectric      1
+special_bonds   lj/coul 0.0 0.0 1.0 
+
+pair_style      hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000  11.5
+bond_style      harmonic  
+angle_style     harmonic  
+dihedral_style  harmonic
+improper_style  none
+kspace_style    pppm 0.001   
+
+read_data       data.dreiding
+
+pair_coeff      1    1    lj/cut/coul/long        0.015200000256300         2.846421344984478 
+pair_coeff      1    2    lj/cut/coul/long        0.001232882795416         2.846421344984478 
+pair_coeff      1    3    lj/cut/coul/long        0.038019995160237         3.159705878878677 
+pair_coeff      1    4    lj/cut/coul/long        0.038139744011598         2.939787518071103 
+pair_coeff      2    2    lj/cut/coul/long     9.99999974737875e-05         2.846421344984478 
+pair_coeff      2    3    lj/cut/coul/long        0.003083828758188         3.159705878878677 
+pair_coeff      2    4    lj/cut/coul/long        0.003093541672406         2.939787518071103 
+pair_coeff      3    3    lj/cut/coul/long        0.095100000500679         3.472990412772877 
+pair_coeff      3    4    lj/cut/coul/long        0.095399530150179         3.253072051965302 
+pair_coeff      4    4    lj/cut/coul/long        0.095700003206730         3.033153691157727 
+pair_coeff      4    4    hbond/dreiding/lj                         2                         i                0.4000E+01         2.750000000000000                         4 
+pair_modify     mix arithmetic
+neighbor        2.0 multi
+neigh_modify    every 2 delay 4 check yes
+variable        input index in.ch3oh.box.dreiding
+variable        sname index ch3oh.box.dreiding
+
+compute   hb all pair hbond/dreiding/lj
+variable    C_hbond equal c_hb[1] #number hbonds
+variable    E_hbond equal c_hb[2] #hbond energy
+thermo_style 	custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify	line multi format float %14.6f
+
+run 0

examples/dreiding/log.dreiding.11Oct11.linux.1

+LAMMPS (10 Oct 2011)
+units           real
+atom_style      full
+boundary        p p p
+dielectric      1
+special_bonds   lj/coul 0.0 0.0 1.0 
+
+pair_style      hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000  11.5
+bond_style      harmonic  
+angle_style     harmonic  
+dihedral_style  harmonic
+improper_style  none
+kspace_style    pppm 0.001   
+
+read_data       data.dreiding
+  4 = max bonds/atom
+  6 = max angles/atom
+  3 = max dihedrals/atom
+  0 = max impropers/atom
+  orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
+  1 by 1 by 1 processor grid
+  384 atoms
+  320 bonds
+  448 angles
+  192 dihedrals
+  0 impropers
+  4 = max # of 1-2 neighbors
+  3 = max # of 1-3 neighbors
+  5 = max # of special neighbors
+
+pair_coeff      1    1    lj/cut/coul/long        0.015200000256300         2.846421344984478 
+pair_coeff      1    2    lj/cut/coul/long        0.001232882795416         2.846421344984478 
+pair_coeff      1    3    lj/cut/coul/long        0.038019995160237         3.159705878878677 
+pair_coeff      1    4    lj/cut/coul/long        0.038139744011598         2.939787518071103 
+pair_coeff      2    2    lj/cut/coul/long     9.99999974737875e-05         2.846421344984478 
+pair_coeff      2    3    lj/cut/coul/long        0.003083828758188         3.159705878878677 
+pair_coeff      2    4    lj/cut/coul/long        0.003093541672406         2.939787518071103 
+pair_coeff      3    3    lj/cut/coul/long        0.095100000500679         3.472990412772877 
+pair_coeff      3    4    lj/cut/coul/long        0.095399530150179         3.253072051965302 
+pair_coeff      4    4    lj/cut/coul/long        0.095700003206730         3.033153691157727 
+pair_coeff      4    4    hbond/dreiding/lj                         2                         i                0.4000E+01         2.750000000000000                         4 
+pair_modify     mix arithmetic
+neighbor        2.0 multi
+neigh_modify    every 2 delay 4 check yes
+variable        input index in.ch3oh.box.dreiding
+variable        sname index ch3oh.box.dreiding
+
+compute   hb all pair hbond/dreiding/lj
+variable    C_hbond equal c_hb[1] #number hbonds
+variable    E_hbond equal c_hb[2] #hbond energy
+thermo_style 	custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify	line multi format float %14.6f
+
+run 0
+WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:204)
+  G vector = 0.142075
+  grid = 3 3 3
+  stencil order = 5
+  RMS precision = 0.000329493
+  using double precision FFTs
+  brick FFT buffer size/proc = 512 27 576
+Memory usage per processor = 7.9487 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =     113.723443 KinEng   =       0.000000 Temp     =       0.000000 
+PotEng   =     113.723443 E_bond   =       0.535673 E_angle  =       1.281880 
+E_dihed  =       1.232497 E_impro  =       0.000000 E_vdwl   =    -125.381324 
+E_coul   =     597.224193 E_long   =    -361.169476 E_hbond  =     -69.322152 
+C_hbond  =     235.000000 Press    =    -847.552598 Volume   =    7447.236335 
+Loop time of 0 on 1 procs for 0 steps with 384 atoms
+
+Pair  time (%) = 0 (0)
+Bond  time (%) = 0 (0)
+Kspce time (%) = 0 (0)
+Neigh time (%) = 0 (0)
+Comm  time (%) = 0 (0)
+Outpt time (%) = 0 (0)
+Other time (%) = 0 (0)
+
+FFT time (% of Kspce) = 0 (0)
+FFT Gflps 3d (1d only) = 0 0
+
+Nlocal:    384 ave 384 max 384 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    4637 ave 4637 max 4637 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    101854 ave 101854 max 101854 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs: 203708 ave 203708 max 203708 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 203708
+Ave neighs/atom = 530.49
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0

examples/dreiding/log.dreiding.11Oct11.linux.4

+LAMMPS (10 Oct 2011)
+units           real
+atom_style      full
+boundary        p p p
+dielectric      1
+special_bonds   lj/coul 0.0 0.0 1.0 
+
+pair_style      hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000  11.5
+bond_style      harmonic  
+angle_style     harmonic  
+dihedral_style  harmonic
+improper_style  none
+kspace_style    pppm 0.001   
+
+read_data       data.dreiding
+  4 = max bonds/atom
+  6 = max angles/atom
+  3 = max dihedrals/atom
+  0 = max impropers/atom
+  orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
+  2 by 1 by 2 processor grid
+  384 atoms
+  320 bonds
+  448 angles
+  192 dihedrals
+  0 impropers
+  4 = max # of 1-2 neighbors
+  3 = max # of 1-3 neighbors
+  5 = max # of special neighbors
+
+pair_coeff      1    1    lj/cut/coul/long        0.015200000256300         2.846421344984478 
+pair_coeff      1    2    lj/cut/coul/long        0.001232882795416         2.846421344984478 
+pair_coeff      1    3    lj/cut/coul/long        0.038019995160237         3.159705878878677 
+pair_coeff      1    4    lj/cut/coul/long        0.038139744011598         2.939787518071103 
+pair_coeff      2    2    lj/cut/coul/long     9.99999974737875e-05         2.846421344984478 
+pair_coeff      2    3    lj/cut/coul/long        0.003083828758188         3.159705878878677 
+pair_coeff      2    4    lj/cut/coul/long        0.003093541672406         2.939787518071103 
+pair_coeff      3    3    lj/cut/coul/long        0.095100000500679         3.472990412772877 
+pair_coeff      3    4    lj/cut/coul/long        0.095399530150179         3.253072051965302 
+pair_coeff      4    4    lj/cut/coul/long        0.095700003206730         3.033153691157727 
+pair_coeff      4    4    hbond/dreiding/lj                         2                         i                0.4000E+01         2.750000000000000                         4 
+pair_modify     mix arithmetic
+neighbor        2.0 multi
+neigh_modify    every 2 delay 4 check yes
+variable        input index in.ch3oh.box.dreiding
+variable        sname index ch3oh.box.dreiding
+
+compute   hb all pair hbond/dreiding/lj
+variable    C_hbond equal c_hb[1] #number hbonds
+variable    E_hbond equal c_hb[2] #hbond energy
+thermo_style 	custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
+thermo_modify	line multi format float %14.6f
+
+run 0
+WARNING: No fixes defined, atoms won't move (verlet.cpp:52)
+PPPM initialization ...
+WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:204)
+  G vector = 0.142075
+  grid = 3 3 3
+  stencil order = 5
+  RMS precision = 0.000329493
+  using double precision FFTs
+WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
+  G vector = 0.143211
+  grid = 3 3 3
+  stencil order = 4
+  RMS precision = 0.000315601
+  using double precision FFTs
+WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
+  G vector = 0.140124
+  grid = 3 3 3
+  stencil order = 3
+  RMS precision = 0.000354326
+  using double precision FFTs
+WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
+  G vector = 0.127333
+  grid = 3 3 3
+  stencil order = 2
+  RMS precision = 0.00055716
+  using double precision FFTs
+WARNING: Reducing PPPM order b/c stencil extends beyond neighbor processor (pppm.cpp:216)
+  G vector = 0.113516
+  grid = 9 9 9
+  stencil order = 1
+  RMS precision = 0.000864991
+  using double precision FFTs
+  brick FFT buffer size/proc = 360 243 360
+Memory usage per processor = 6.52575 Mbytes
+---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
+TotEng   =     118.484313 KinEng   =       0.000000 Temp     =       0.000000 
+PotEng   =     118.484313 E_bond   =       0.535673 E_angle  =       1.281880 
+E_dihed  =       1.232497 E_impro  =       0.000000 E_vdwl   =    -125.381324 
+E_coul   =     529.430008 E_long   =    -288.614421 E_hbond  =     -69.322152 
+C_hbond  =     235.000000 Press    =    -803.848888 Volume   =    7447.236335 
+Loop time of 1.43051e-06 on 4 procs for 0 steps with 384 atoms
+
+Pair  time (%) = 0 (0)
+Bond  time (%) = 0 (0)
+Kspce time (%) = 0 (0)
+Neigh time (%) = 0 (0)
+Comm  time (%) = 0 (0)
+Outpt time (%) = 0 (0)
+Other time (%) = 1.43051e-06 (100)
+
+FFT time (% of Kspce) = 0 (0)
+FFT Gflps 3d (1d only) = 0 0
+
+Nlocal:    96 ave 104 max 87 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:    3063.25 ave 3108 max 3024 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    25463.5 ave 28799 max 22471 min
+Histogram: 1 0 0 1 0 1 0 0 0 1
+FullNghs: 50927 ave 55516 max 46073 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 203708
+Ave neighs/atom = 530.49
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0