Merge pull request #53 from lammpstutorials/adress-warning-tutorial4

Deal with warning in tutorial 4

Author: simongravelle

figures/NANOSHEAR-equilibration.png

@@ -12,7 +12,7 @@ pair_style lj/cut/tip4p/long O H O-H H-O-H 0.1546 12.0
 kspace_style pppm/tip4p 1.0e-5
 kspace_modify slab 3.0
 
-read_data minimize.data
+read_data create.data
 
 include parameters.inc
 include groups.inc

files/tutorial4/equilibrate.lmp

@@ -1,14 +1,13 @@
   using 8 OpenMP thread(s) per MPI task
 using multi-threaded neighbor list subroutines
-WARNING: Detected non-ASCII characters in input. Will try to continue by replacing with ASCII equivalents where known. (src/input.cpp:478)
 Lattice spacing in x,y,z = 4.04 4.04 4.04
 Created orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
   1 by 1 by 1 MPI processor grid
 Created 432 atoms
   using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
   create_atoms CPU = 0.006 seconds
 Read molecule template h2omol:
-# Water molecule.
+# LAMMPS Input File (License CC BY 4.0)
   1 molecules
   0 fragments
   3 atoms with max type 2
@@ -21,7 +20,7 @@ Created 1944 atoms
   create_atoms CPU = 0.002 seconds
 Created 15 atoms
   using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
-  create_atoms CPU = 0.004 seconds
+  create_atoms CPU = 0.005 seconds
 Created 15 atoms
   using lattice units in orthogonal box = (-12.12 -12.12 -20.2) to (12.12 12.12 20.2)
   create_atoms CPU = 0.004 seconds
@@ -63,7 +62,7 @@ PPPM initialization ...
   estimated relative force accuracy = 1.0535666e-05
   using double precision KISS FFT
   3d grid and FFT values/proc = 39375 19440
-WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:731)
+WARNING: Communication cutoff 0 is shorter than a bond length based estimate of 3.4358. This may lead to errors. (src/comm.cpp:730)
 WARNING: Increasing communication cutoff to 15.1118 for TIP4P pair style (src/KSPACE/pair_lj_cut_tip4p_long.cpp:497)
 Generated 9 of 10 mixed pair_coeff terms from geometric mixing rule
 Last active /omp style is kspace_style pppm/tip4p/omp
@@ -86,9 +85,9 @@ Setting up Verlet run ...
 Per MPI rank memory allocation (min/avg/max) = 19.16 | 19.16 | 19.16 Mbytes
    Step          Temp          E_pair         E_mol          TotEng         Press     
          0   0              501411.03      0              501411.03      6165751.9    
-Loop time of 0.000133443 on 8 procs for 0 steps with 1680 atoms
+Loop time of 3.207e-06 on 8 procs for 0 steps with 1680 atoms
 
-81.7% CPU use with 1 MPI tasks x 8 OpenMP threads
+155.9% CPU use with 1 MPI tasks x 8 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
@@ -100,7 +99,7 @@ Neigh   | 0          | 0          | 0          |   0.0 |  0.00
 Comm    | 0          | 0          | 0          |   0.0 |  0.00
 Output  | 0          | 0          | 0          |   0.0 |  0.00
 Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.0001334  |            |       |100.00
+Other   |            | 3.207e-06  |            |       |100.00
 
 Nlocal:           1680 ave        1680 max        1680 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

files/tutorial4/minimize.lmp

@@ -12,16 +12,34 @@ pair_style lj/cut/tip4p/long O H O-H H-O-H 0.1546 12.0
 kspace_style pppm/tip4p 1.0e-5
 kspace_modify slab 3.0
 
-read_data minimize.data
+read_data create.data
 
 include parameters.inc
 include groups.inc
 
+fix myshk H2O shake 1.0e-5 200 0 b O-H a H-O-H kbond 2000
+
+dump mydmp all image 1 myimage-*.ppm type type &
+  shiny 0.1 box no 0.01 view 90 0 zoom 1.8
+dump_modify mydmp backcolor white &
+  acolor O red adiam O 2 &
+  acolor H white adiam H 1 &
+  acolor Na+ blue adiam Na+ 2.5 &
+  acolor Cl- cyan adiam Cl- 3 &
+  acolor WALL gray adiam WALL 3
+
+thermo 1
+thermo_style custom step temp etotal press
+
+minimize 1.0e-6 1.0e-6 1000 1000
+reset_timestep 0
+
 fix mynvt all nvt temp 300 300 100
 fix myshk H2O shake 1.0e-5 200 0 b O-H a H-O-H
 fix myrct all recenter NULL NULL 0
 timestep 1.0
 
+undump mydmp
 dump mydmp all image 250 myimage-*.ppm type type &
   shiny 0.1 box no 0.01 view 90 0 zoom 1.8
 dump_modify mydmp backcolor white &
@@ -41,3 +59,7 @@ thermo_style custom step temp etotal press v_deltaz
 run 30000
 
 write_data equilibrate.data nocoeff
+
+
+
+