[DFTB-Plus-User] [Fwd: MD periodic problem]

Thu Nov 5 05:07:44 CET 2009

Hi All,

I just started using DFTB+. I am trying to do a MD calculation with 
periodic option.  This is disordered system (liquid like).   I see some 
of the atoms/molecules are going out from the box and the cartesian 
coordinates it prints are not within the box.  I am under the impression 
that if an tries to go out from the box, it will be replaced by another 
(image) so that the total number of atoms will be unchanged in the box.
I was wondering if anyone can help.  I have attached a sample input and 
final atom coordinates.  Thanks
Debasis

Geometry = GenFormat {
  35  F
 H  N  C  O
1  4      0.11181      0.26931      0.20139
2  2      0.11801      0.16872      0.18947
3  4      0.05346      0.10511      0.11419
4  4      0.21510      0.11723      0.26701
5  1      0.26855      0.17667      0.32115
6  4      0.67988      0.26552      0.44556
7  2      0.72678      0.22944      0.56835
8  4      0.81813      0.17204      0.57413
9  4      0.66519      0.25044      0.71377
10  1      0.58444      0.28870      0.69496
11  1      0.95983      0.59924      0.23409
12  3      0.91145      0.57768      0.34634
13  2      0.78306      0.60489      0.34106
14  1      0.95137      0.62003      0.45452
15  1      0.92169      0.48939      0.36866
16  3      0.71782      0.64309      0.47499
17  3      0.71311      0.59615      0.20846
18  2      0.60055      0.64325      0.42501
19  1      0.74795      0.66598      0.59967
20  3      0.59431      0.61012      0.26246
21  1      0.74298      0.57803      0.08588
22  3      0.50342      0.67841      0.52870
23  2      0.33653      0.44067      0.78564
24  1      0.50503      0.58426      0.20657
25  1      0.48317      0.61143      0.61903
26  1      0.42664      0.69174      0.44186
27  3      0.54163      0.78123      0.61005
28  3      0.31147      0.38449      0.65800
29  3      0.33177      0.53887      0.85398
30  1      0.60934      0.82420      0.53416
31  3      0.52022      0.82262      0.76248
32  2      0.28748      0.33070      0.53578
33  2      0.33665      0.62179      0.92928
34  1      0.46991      0.78062      0.86108
35  1      0.56319      0.90377      0.80362
     0.00000000      0.00000000      0.00000000
    11.00000000      0.00000000      0.00000000
     0.00000000     12.00000000      0.00000000
     0.00000000      0.00000000      8.00000000
}

Driver = VelocityVerlet {
 Steps = 5000
 TimeStep [Femtosecond] = 1.00000000000000
 Thermostat = None {
   InitialTemperature [Kelvin] = 1000.00
 }
 OutputPrefix = "geo_end"
 MDRestartFrequency = 20
}
Hamiltonian = DFTB {
 SCC = Yes
 SCCTolerance = 1e-3
 MaxAngularMomentum = {
   C = "p"
   O = "p"
   N = "p"
   H = "s"
 }
 Charge = 0.000000000000000E+000
 SpinPolarisation = {}
 Eigensolver = Standard {}
 Filling = Fermi {
   Temperature [Kelvin] = 116.045
 }
 SlaterKosterFiles = Type2FileNames{
   Prefix = "../../mio-0-1/"
   Separator = "-"
   Suffix = ".skf"
 }

 KPointsAndWeights = {
 0.0 0.0 0.0 1.0
 }
 ReadInitialCharges = No
}

Options = {
 WriteAutotestTag = Yes
 RandomSeed = 12345
}

ParserOptions = {
 ParserVersion = 3
}

***************************
  35  F
 H  N  C  O
   1 4      0.98514762     -0.08732773      0.34321459
   2 2      1.00225705     -0.06939687      0.49571980
   3 4      1.11966336     -0.06355991      0.53762296
   4 4      0.91668536     -0.06431552      0.60039665
   5 1      0.66286244      0.55781037      1.18944395
   6 4      0.77406651     -0.21221520      0.85229500
   7 2      0.69212031     -0.19449710      0.76767971
   8 4      0.71280931     -0.17418792      0.59635634
   9 4      0.58097677     -0.20780609      0.79520981
  10 1      0.80912563     -0.14279970      0.59730408
  11 1      0.36054637      0.83697061     -0.09439308
  12 3      0.27133797      0.84226427     -0.16542980
  13 2      0.19182650      0.91823321     -0.05203348
  14 1      0.20989743      0.77320339     -0.19204116
  15 1      0.27930990      0.90792566     -0.26062747
  16 3      0.07837409      0.94866225     -0.09694924
  17 3      0.22211929      0.97960977      0.08852895
  18 2      0.04516267      1.02917556      0.00105256
  19 1      0.01609527      0.91950446     -0.20277805
  20 3      0.13250746      1.05564772      0.11690151
  21 1      0.30835623      0.96059499      0.14936010
  22 3     -0.08586758      1.06911641      0.00027154
  23 2      0.66098868      0.47522382      1.12045398
  24 1      0.10028376      1.09165591      0.24084794
  25 1     -0.13163054      1.00341238     -0.07608299
  26 1     -0.10736443      1.14145272     -0.08381814
  27 3     -0.12958266      1.09920112      0.16970947
  28 3      0.70360756      0.45339342      0.95983339
  29 3      0.55911535      0.42034628      1.18463850
  30 1     -0.12350537      1.03794370      0.26152572
  31 3     -0.18995221      1.19186232      0.20749785
  32 2      0.73817643      0.42857365      0.83321195
  33 2      0.47336102      0.37554519      1.22544599
  34 1     -0.21856864      1.25111387      0.10055344
  35 1     -0.21262486      1.20965944      0.33761876
     0.00000000      0.00000000      0.00000000
    11.00000000      0.00000000      0.00000000
     0.00000000     12.00000000      0.00000000
     0.00000000      0.00000000      8.00000000

-- 
Debasis Sengupta, Ph.D
CFD Research Corporation
Chemical and Materials Technology
215 Wynn Drive, Huntsville, AL 35805
Ph: 908-752-4843
Fax: 256-726-4806 
http://www.cfdrc.com

-- 
Debasis Sengupta, Ph.D
CFD Research Corporation
Chemical and Materials Technology
215 Wynn Drive, Huntsville, AL 35805
Ph: 908-752-4843
Fax: 256-726-4806 
http://www.cfdrc.com