Hi,
I have built a small system of pentane and I am getting the following output for the enclosed
files. I am running the windows lamps executable for serial execution. I’m concerned with the
warning message prior to minimization. Temperature and pressure do not converge to 160 K and 1
atm respectively.
Any insight is much appreciated.
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C:\winlaamps>lmps.exe < five.txt
LAMMPS (21 Dec 2010)
Scanning data file …
4 = max bonds/atom
6 = max angles/atom
16 = max dihedrals/atom
4 = max impropers/atom
Reading data file …
orthogonal box = (-11.008 -2.013 -1.633) to (-5.141 1.397 1.369)
1 by 1 by 1 processor grid
17 atoms
16 bonds
30 angles
36 dihedrals
20 impropers
Finding 1-2 1-3 1-4 neighbors …
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
16 = max # of special neighbors
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization …
Memory usage per processor = 8.0564 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 20891.468 -2.0792724 20889.388 71198096
29 0 298.39464 -1613.3609 -1314.9663 1120861.9
Loop time of 0.0459051 on 1 procs for 29 steps with 17 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
20889.3884407 -1314.96630841 -1314.96630841
Force two-norm initial, final = 239658 902.098
Force max component initial, final = 123078 529.267
Final line search alpha, max atom move = 1.09978e-014 5.82077e-012
Iterations, force evaluations = 29 323
Pair time () = 0.0019511 (4.25028)
Bond time () = 0.0351563 (76.5846)
Neigh time () = 0 (0)
Comm time () = 0.0068326 (14.8842)
Outpt time () = 0 (0)
Other time () = 0.00196515 (4.28089)
Nlocal: 17 ave 17 max 17 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 587 ave 587 max 587 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 386 ave 386 max 386 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 386
Ave neighs/atom = 22.7059
Ave special neighs/atom = 9.64706
Neighbor list builds = 0
Dangerous builds = 0
Setting up run …
Memory usage per processor = 7.36858 Mbytes
Step Temp Press E_mol Volume
29 0 1120861.9 -1613.3609 60.059423
100 414.19644 -8635.304 -1891.8495 195.96301
200 106.44843 5287.5454 -1908.0921 201.34868
300 69.053713 3697.3763 -1906.8254 188.26264
400 80.192383 -8906.2675 -1905.6304 194.51575
500 93.520084 -3405.5872 -1904.6722 178.37182
600 107.82918 -2587.4576 -1904.1197 193.65009
700 159.75022 -5813.4336 -1906.0181 218.13632
800 136.24884 -278.59456 -1904.4372 218.77855
900 162.86559 -8056.119 -1905.6883 211.32461
1000 159.5775 2552.1636 -1904.9643 215.84569
1029 186.98932 1364.0935 -1906.3382 218.71168
Loop time of 0.140645 on 1 procs for 1000 steps with 17 atoms
Pair time () = 0.00390687 (2.77782)
Bond time () = 0.116229 (82.6399)
Neigh time () = -2.01282e-007 (-0.000143113)
Comm time () = 0.00292909 (2.08261)
Outpt time () = 0.0126971 (9.02777)
Other time () = 0.00488332 (3.47208)
Nlocal: 17 ave 17 max 17 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 259 ave 259 max 259 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 59 ave 59 max 59 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 59
Ave neighs/atom = 3.47059
Ave special neighs/atom = 9.64706
Neighbor list builds = 6
Dangerous builds = 4
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% five.txt %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%5
LAMMPS is always 3D unless you are doing a specific 2D project
#====================== UNITS =========================
#Always good to know your units up front
units real
#====================== OUTPUT Section =========================
#Define what you want from the simulation up front
dump 1 all atom 100 c:\winlaamps\dump.five
#====================== MD Cell properties =====================
#define the read template to read in the atoms from the geometry
#file
atom_style full
#Define a periodic MD cell in all dimensions
#coordinate this with the MD cell in the include file in the
#read_data statement below
boundary p p p
#====================== Force Field Specification ===============
#The bonded and non-bonded data must be specified prior to the
#read_data statement below
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
pair_style lj/class2/coul/cut 2.5
pair_modify mix sixthpower
#====================== Geometry Specification ================
#Read in the geometry
read_data five.lammps05
#====================== Molecular Mechanics ================
#Define the algorithm for minimization
min_style sd
minimize 1.0e-12 1.0e-6 1000000 1000000
#====================== Molecular Dynamics ================