[CPMD-list] Help with molecular crystals -- atoms are too close
okan.esenturk at nist.gov
okan.esenturk at nist.gov
Mon Oct 2 17:10:52 CEST 2006
Hi all,
I am new on using CPMD.
I am trying to run the following input file..
------input starts
&INFO
xxx
&END
&CPMD
VIBRATIONAL ANALYSIS FD GAUSS SAMPLE
2
PRINT LSCAL ON
CENTER MOLECULE OFF
STRUCTURE BONDS ANGLES
&END
&DFT
FUNCTIONAL BLYP
GC-CUTOFF
1.0d-6
&END
&SYSTEM
POINT GROUP DELTA=1.0E-6
AUTO
ANGSTROM
SYMMETRY
ORTHORHOMBIC
CELL ABSOLUTE DEGREE
12.584 3.894 6.955 90.0 90.0 90.0
CUTOFF SPHERICAL
90.0
&END
&ATOMS
*C_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=P
24
0.701000000 0.777000000 1.075000000
6.993000000 3.117000000 4.552000000
5.591000000 3.117000000 4.552000000
11.883000000 0.777000000 1.075000000
13.285000000 0.777000000 1.075000000
-0.701000000 0.777000000 1.075000000
4.913000000 3.648000000 3.478000000
11.205000000 0.246000000 0.000000000
-1.379000000 0.246000000 0.000000000
1.379000000 0.246000000 0.000000000
7.671000000 3.648000000 3.478000000
13.963000000 0.246000000 0.000000000
-0.698000000 -0.258000000 -1.056000000
0.698000000 -0.258000000 -1.056000000
11.886000000 -0.258000000 -1.056000000
5.594000000 4.152000000 2.421000000
13.282000000 -0.258000000 -1.056000000
6.990000000 4.152000000 2.421000000
13.993000000 1.332000000 2.185000000
-1.409000000 1.332000000 2.185000000
4.883000000 2.562000000 5.663000000
1.409000000 1.332000000 2.185000000
7.701000000 2.562000000 5.663000000
11.175000000 1.332000000 2.185000000
*N_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=P
6
14.570000000 1.772000000 3.077000000
1.986000000 1.772000000 3.077000000
8.278000000 2.122000000 6.554000000
-1.986000000 1.772000000 3.077000000
10.598000000 1.772000000 3.077000000
4.306000000 2.122000000 6.554000000
*H_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=S
12
8.670000000 3.547000000 3.491000000
10.206000000 0.347000000 0.014000000
14.962000000 0.347000000 0.014000000
2.378000000 0.347000000 0.014000000
3.914000000 3.547000000 3.491000000
-2.378000000 0.347000000 0.014000000
1.195000000 -0.639000000 -1.836000000
-1.195000000 -0.639000000 -1.836000000
13.779000000 -0.639000000 -1.836000000
11.389000000 -0.639000000 -1.836000000
5.097000000 4.533000000 1.641000000
7.487000000 4.533000000 1.641000000
&END
----------input ends
This input file is made from crystal data using Mercury. It has three full
molecules. Crystal unit only has two (Z=2) but I did not want to input partial
molecules. It is an orthorhombic unit with the given unit cell parameters.
I have not optimized the geometry or wavefunction. I'd like to calculate the
crystal phonon modes of the structure. Optimizing geometry will change the
distances and symmetry, I believe.
I have also tried with standard potential comes with the CPMD but both fails
in the same place reporting atoms are too close. I've checked the given
coordinates (from the input file or from the output file) to make sure and all
the atoms are in proper distances from each other.
Would anybody know why I would receive such an error and the why it is
not properly running. output file is given below.
Thanks you very much.
Okan Esenturk
info: running on multi processor MPI-LAM system. Compiled for 64 bit
opteron and xeon systems. Using version CPMD 3.11.1.
--------- output file
VERSION 3.11.1
PERFORM A VIBRATIONAL ANALYSIS BY FINITE DIFFERENCES
PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 10000 STEPS
STEP SIZE FOR FINITE DIFFERENCES (BOHR): 1.0000E-02
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK
BEHAVIOR
FICTITIOUS ELECTRON MASS: 400.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
ALL VIBRATIONAL FREQUENCIES AND EIGENVECTORS ARE
SAVED IN GAUSSIAN-STYLE FORMATTED FILES
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION:
1.0000E-07
CONVERGENCE CRITERIA FOR WAVEFUNCTION RELATIVE TO
GRADIENT ON IONS: 2.0000E-02
CONVERGENCE CRITERIA FOR RELAVTIVE WAVEFUNCTION
ENERGY CHANGE: 5.0000E-02
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
THRESHOLD FOR THE WF-HESSIAN IS 0.5000
MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 5
STEPS UNTIL DIIS RESET ON POOR PROGRESS: 30
FULL ELECTRONIC GRADIENT IS USED
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL
FUNCTIONS
NUMBER OF SPLINE POINTS: 5000
EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: SLATER (ALPHA = 0.66667)
LDA CORRELATION: LEE, YANG & PARR
[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 1.00000E-06
EXCHANGE ENERGY
[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
PARAMETER BETA: 0.004200
CORRELATION ENERGY
[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]
*** DETSP| SIZE OF THE PROGRAM IS 2684/ 78296 kBYTES ***
AUTOMATIC DETERMINATION OF THE POINT GROUP:
THE CRYSTAL SYSTEM IS ORTHORHOMBIC WITH 2 OPERATIONS:
1 -2[ 1 0 0]
THE SPACE GROUP OF THE CRYSTAL IS SYMMORPHIC
THE POINT GROUP OF THE CRYSTAL IS m(c1h) [INDEX= 4]
NUMBER OF PRIMITIVE CELLS: 2
TRANSLATION VECTORS:
TVEC( 1): [ 0.000, 0.000, 0.000]
TVEC( 2): [ 0.000, 0.000, 0.000]
SYMMETRY UNIQUE (INEQUIVALENT) ATOMS: 28
INDEXES: 1 2 5 6 7 8 9 12 13 15
16 17 19 21 22 24 25 26 27 29 31
32 34 36 37 39 40 41
REQUIRED PRECISION FOR SYMMETRY: 1.00E-06
MULTTB| SUPERCELL ATOMS FORM NO BASIS FOR THIS POINT
GROUP
NUMBER OF IRREDUCIBLE REPRESENTATIONS: 2
DIMENSION OF IR: 1 1
***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 C 1.324698 1.468317 2.031455 3
2 C 13.214854 5.890276 8.602033 3
3 C 10.565458 5.890276 8.602033 3
4 C 22.455614 1.468317 2.031455 3
5 C 25.105010 1.468317 2.031455 3
6 C -1.324698 1.468317 2.031455 3
7 C 9.284224 6.893720 6.572467 3
8 C 21.174380 0.464873 0.000000 3
9 C -2.605932 0.464873 0.000000 3
10 C 2.605932 0.464873 0.000000 3
11 C 14.496088 6.893720 6.572467 3
12 C 26.386244 0.464873 0.000000 3
13 C -1.319029 -0.487549 -1.995551 3
14 C 1.319029 -0.487549 -1.995551 3
15 C 22.461283 -0.487549 -1.995551 3
16 C 10.571127 7.846142 4.575027 3
17 C 25.099341 -0.487549 -1.995551 3
18 C 13.209185 7.846142 4.575027 3
19 C 26.442936 2.517115 4.129051 3
20 C -2.662624 2.517115 4.129051 3
21 C 9.227532 4.841478 10.701518 3
22 C 2.662624 2.517115 4.129051 3
23 C 14.552780 4.841478 10.701518 3
24 C 21.117688 2.517115 4.129051 3
25 N 27.533308 3.348594 5.814687 3
26 N 3.752996 3.348594 5.814687 3
27 N 15.643152 4.009999 12.385264 3
28 N -3.752996 3.348594 5.814687 3
29 N 20.027316 3.348594 5.814687 3
30 N 8.137160 4.009999 12.385264 3
31 H 16.383924 6.702858 6.597033 3
32 H 19.286543 0.655735 0.026456 3
33 H 28.274080 0.655735 0.026456 3
34 H 4.493768 0.655735 0.026456 3
35 H 7.396388 6.702858 6.597033 3
36 H -4.493768 0.655735 0.026456 3
37 H 2.258223 -1.207535 -3.469537 3
38 H -2.258223 -1.207535 -3.469537 3
39 H 26.038534 -1.207535 -3.469537 3
40 H 21.522089 -1.207535 -3.469537 3
41 H 9.631933 8.566MPI_Recv: process in local group is dead
(rank 3, comm 3)
MPI_Recv: process in local group is dead (rank 5, comm 3)
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (3, MPI_COMM_WORLD): Call stack within LAM:
Rank (3, MPI_COMM_WORLD): - MPI_Recv()
Rank (3, MPI_COMM_WORLD): - MPI_Bcast()
Rank (3, MPI_COMM_WORLD): - MPI_Bcast()
Rank (3, MPI_COMM_WORLD): - main()
128 3.101040 3
42 H 14.148378 8.566128 3.101040 3
****************************************************************
ATOM TYPE= 1 NUM= 1 1.324697917993825
1.468317093125823 2.031455437722343
ATOM TYPE= 1 NUM= 5 25.10500975827100
1.468317093125823 2.031455437722343
PROGRAM STOPS IN SUBROUTINE SETSYS| ATOMS ARE VERY
CLOSE [PROC= 0]
MPI_Recv: process in local group is dead (rank 6, comm 3)
Rank (10, MPI_COMM_WORLD): Call stack within LAM:
Rank (10, MPI_COMM_WORLD): - MPI_Recv()
Rank (10, MPI_COMM_WORLD): - MPI_Bcast()
Rank (10, MPI_COMM_WORLD): - MPI_Bcast()
Rank (10, MPI_COMM_WORLD): - main()
Rank (6, MPI_COMM_WORLD): Call stack within LAM:
Rank (6, MPI_COMM_WORLD): - MPI_Recv()
Rank (6, MPI_COMM_WORLD): - MPI_Bcast()
Rank (6, MPI_COMM_WORLD): - MPI_Bcast()
Rank (6, MPI_COMM_WORLD): - main()
MPI_Recv: process in local group is dead (rank 7, comm 3)
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (5, MPI_COMM_WORLD): Call stack within LAM:
Rank (5, MPI_COMM_WORLD): - MPI_Recv()
Rank (5, MPI_COMM_WORLD): - MPI_Bcast()
Rank (5, MPI_COMM_WORLD): - MPI_Bcast()
Rank (5, MPI_COMM_WORLD): - main()
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (9, MPI_COMM_WORLD): Call stack within LAM:
Rank (9, MPI_COMM_WORLD): - MPI_Recv()
Rank (9, MPI_COMM_WORLD): - MPI_Bcast()
Rank (9, MPI_COMM_WORLD): - MPI_Bcast()
Rank (9, MPI_COMM_WORLD): - main()
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (7, MPI_COMM_WORLD): Call stack within LAM:
Rank (7, MPI_COMM_WORLD): - MPI_Recv()
Rank (7, MPI_COMM_WORLD): - MPI_Bcast()
Rank (7, MPI_COMM_WORLD): - MPI_Bcast()
Rank (7, MPI_COMM_WORLD): - main()
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (11, MPI_COMM_WORLD): Call stack within LAM:
Rank (11, MPI_COMM_WORLD): - MPI_Recv()
Rank (11, MPI_COMM_WORLD): - MPI_Bcast()
Rank (11, MPI_COMM_WORLD): - MPI_Bcast()
Rank (11, MPI_COMM_WORLD): - main()
Rank (14, MPI_COMM_WORLD): Call stack within LAM:
Rank (14, MPI_COMM_WORLD): - MPI_Recv()
Rank (14, MPI_COMM_WORLD): - MPI_Bcast()
Rank (14, MPI_COMM_WORLD): - MPI_Bcast()
Rank (14, MPI_COMM_WORLD): - main()
Rank (12, MPI_COMM_WORLD): Call stack within LAM:
Rank (12, MPI_COMM_WORLD): - MPI_Recv()
Rank (12, MPI_COMM_WORLD): - MPI_Bcast()
Rank (12, MPI_COMM_WORLD): - MPI_Bcast()
Rank (12, MPI_COMM_WORLD): - main()
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (15, MPI_COMM_WORLD): Call stack within LAM:
Rank (15, MPI_COMM_WORLD): - MPI_Recv()
Rank (15, MPI_COMM_WORLD): - MPI_Bcast()
Rank (15, MPI_COMM_WORLD): - MPI_Bcast()
Rank (15, MPI_COMM_WORLD): - main()
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm
for CID 0)
Rank (13, MPI_COMM_WORLD): Call stack within LAM:
Rank (13, MPI_COMM_WORLD): - MPI_Recv()
Rank (13, MPI_COMM_WORLD): - MPI_Bcast()
Rank (13, MPI_COMM_WORLD): - MPI_Bcast()
Rank (13, MPI_COMM_WORLD): - main()
NIST, Optical Technology Division
301 975 825
okan.esenturk at nist.gov
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