 Re: The problem of RF constrained optimization with patch 3.8.4 and 3.8.5 ( No.1 ) |
- Date: 2019/03/26 10:44
- Name: Alisa
- And this is the patch 3.8.5 to openmx VER. 3.8.
#
# File Name
#
DATA.PATH /home/ISSP2/zhang/software/openmx3.8/DFT_DATA13
System.CurrrentDirectory ./ # default=./
System.Name tepb56
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (1-3)
#
# restart using a restart file, *.rst
#
scf.restart on
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
Pb Pb8.0-s2p2d2f1 Pb_PBE13
Te Te7.0-s2p2d2 Te_PBE13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.Number 56
Atoms.SpeciesAndCoordinates.Unit FRAC # Ang|AU
<Atoms.SpeciesAndCoordinates # Unit=Ang.
1 Te -0.00004929931693 0.00004136435179 0.09395308508963 8.0 8.0
2 Te 0.99618168345906 0.00283905377664 0.28516370647373 8.0 8.0
3 Te 0.99476511296405 -0.00520743412187 0.47859340708723 8.0 8.0
4 Te 0.24998783916617 0.25000598138130 -0.00000536868474 8.0 8.0
5 Te 0.24961441767005 0.25021915634945 0.18783517825691 8.0 8.0
6 Te 0.24494078310218 0.25235983075125 0.38274042402051 8.0 8.0
7 Te 0.24256288558059 0.24612784519617 0.57747770386805 8.0 8.0
8 Te 0.49994727157178 0.00004073350737 0.09392229416422 8.0 8.0
9 Te 0.49556767945876 0.00260130998226 0.28434849115701 8.0 8.0
10 Te 0.49478827226989 0.00099518772067 0.47481109418778 8.0 8.0
11 Te 0.74999480367857 0.25000591497308 -0.00000473128344 8.0 8.0
12 Te 0.74974825171326 0.25020632422899 0.18784672826836 8.0 8.0
13 Te 0.74575189460068 0.25143942208819 0.38276105913882 8.0 8.0
14 Te 0.74615267424380 0.24636885188654 0.57720297117837 8.0 8.0
15 Te -0.00005091825944 0.50002150513560 0.09395600098702 8.0 8.0
16 Te 0.99562581807385 0.50292263001391 0.28507513462405 8.0 8.0
17 Te 0.99482507713978 0.50115789248919 0.47814970407472 8.0 8.0
18 Te 0.24998782338967 0.75000463424652 -0.00000812054594 8.0 8.0
19 Te 0.24960836230219 0.75018127605167 0.18778473734687 8.0 8.0
20 Te 0.24581401809451 0.75141032886277 0.38385643071764 8.0 8.0
21 Te 0.24714961735202 0.74616763631577 0.57958608660614 8.0 8.0
22 Te 0.49994847979173 0.50002216267191 0.09393068917950 8.0 8.0
23 Te 0.49604531262481 0.50325864372207 0.28418309721225 8.0 8.0
24 Te 0.49452045933262 0.49522719278767 0.47431663915233 8.0 8.0
25 Te 0.74999482575950 0.75000469654941 -0.00000924703821 8.0 8.0
26 Te 0.74975832877543 0.75019315386830 0.18775655191761 8.0 8.0
27 Te 0.74512542537815 0.75192134715444 0.38367831732749 8.0 8.0
28 Te 0.74158148224993 0.74617665862082 0.57954528885485 8.0 8.0
29 Pb -0.00000987898148 0.00000777759772 -0.00000280309811 7.0 7.0
30 Pb -0.00034048640745 0.00024922798140 0.18800610347655 7.0 7.0
31 Pb 0.99593089697326 0.00185484653681 0.37942545741118 7.0 7.0
32 Pb 0.99434719429185 -0.00422998217432 0.56994171978384 7.0 7.0
33 Pb 0.24992488781385 0.25004058452244 0.09393414697785 7.0 7.0
34 Pb 0.24548992011162 0.25316943386534 0.28509352100879 7.0 7.0
35 Pb 0.24050495176244 0.24792888365603 0.48144838079867 7.0 7.0
36 Pb 0.49998987361815 0.00000776154404 -0.00001028272095 7.0 7.0
37 Pb 0.49963868395764 0.00024304721424 0.18786101965544 7.0 7.0
38 Pb 0.49514747067924 0.00343343164136 0.37774814667000 7.0 7.0
39 Pb 0.49444695054777 0.00616870562636 0.56489466078718 7.0 7.0
40 Pb 0.74995546109764 0.25004077717658 0.09393563316896 7.0 7.0
41 Pb 0.74616136316765 0.25257892085753 0.28510950896986 7.0 7.0
42 Pb 0.74893388394299 0.24804431478462 0.48129262188719 7.0 7.0
43 Pb -0.00000987426867 0.50000449916767 -0.00000197358509 7.0 7.0
44 Pb -0.00035282600576 0.50018865010728 0.18801910070791 7.0 7.0
45 Pb 0.99522066096724 0.50215734352676 0.37923279174304 7.0 7.0
46 Pb 0.99438847518853 0.49696124644489 0.56954922533797 7.0 7.0
47 Pb 0.24992445413055 0.75003399595611 0.09392148602591 7.0 7.0
48 Pb 0.24563054027703 0.75272292435914 0.28457154778358 7.0 7.0
49 Pb 0.24884526823087 0.74801523434397 0.47984018176309 7.0 7.0
50 Pb 0.49998984682966 0.50000450942609 -0.00000859826480 7.0 7.0
51 Pb 0.49964783196093 0.50019404777896 0.18790166303639 7.0 7.0
52 Pb 0.49589908336659 0.50067093122984 0.37750160404473 7.0 7.0
53 Pb 0.49428978544424 0.48657549151272 0.56448543541937 7.0 7.0
54 Pb 0.74995635764488 0.75003362848000 0.09391724673298 7.0 7.0
55 Pb 0.74618943312136 0.75323215543889 0.28452833309545 7.0 7.0
56 Pb 0.74061296782963 0.74799932894844 0.47974476464936 7.0 7.0
Atoms.SpeciesAndCoordinates>
<MD.Fixed.XYZ
1 1 1 1
2 0 0 0
3 0 0 0
4 1 1 1
5 1 1 1
6 0 0 0
7 0 0 0
8 1 1 1
9 0 0 0
10 0 0 0
11 1 1 1
12 1 1 1
13 0 0 0
14 0 0 0
15 1 1 1
16 0 0 0
17 0 0 0
18 1 1 1
19 1 1 1
20 0 0 0
21 0 0 0
22 1 1 1
23 0 0 0
24 0 0 0
25 1 1 1
26 1 1 1
27 0 0 0
28 0 0 0
29 1 1 1
30 1 1 1
31 0 0 0
32 0 0 0
33 1 1 1
34 0 0 0
35 0 0 0
36 1 1 1
37 1 1 1
38 0 0 0
39 0 0 0
40 1 1 1
41 0 0 0
42 0 0 0
43 1 1 1
44 1 1 1
45 0 0 0
46 0 0 0
47 1 1 1
48 0 0 0
49 0 0 0
50 1 1 1
51 1 1 1
52 0 0 0
53 0 0 0
54 1 1 1
55 0 0 0
56 0 0 0
MD.Fixed.XYZ>
Atoms.UnitVectors.Unit AU
<Atoms.UnitVectors
17.264196480979098 0.000000000000000 0.000000000000000
0.000000000000000 17.264196480979098 0.000000000000000
0.000000000000000 0.000000000000000 64.968781377069377
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW
scf.SpinPolarization off # On|Off
scf.ElectronicTemperature 600.0 # default=300 (K)
scf.energycutoff 300.0 # default=150 (Ry)
scf.maxIter 170 # default=40
scf.EigenvalueSolver band # Recursion|Cluster|Band
scf.Kgrid 4 4 1 # means 4x4x4
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay
scf.Init.Mixing.Weight 0.010 # default=0.3
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.4
scf.Mixing.History 30 # default=5
scf.Mixing.StartPulay 30 # default=6
scf.criterion 3.0e-8 # default=1.0e-6 (Hartree)
scf.system.charge 0.0 # default=0.0
#
# MD or Geometry Optimization
#
MD.Type RF # Nomd|Opt|DIIS|NVE|NVT_VS|NVT_NH
MD.Opt.DIIS.History 7 # default=7
MD.Opt.StartDIIS 5 # default=5
MD.Opt.EveryDIIS 5 # default=5
MD.TimeStep 0.1 # default=0.5(fs)
MD.maxIter 200 # default=1
MD.Opt.criterion 2.0e-4 # default=1.0e-4 (Hartree/bohr)
#
# output Hamiltonian and overlap
#
HS.fileout on # on|off, default=off
Thank you very much
 |
| Re: The problem of RF constrained optimization with patch 3.8.4 and 3.8.5 ( No.2 ) |
- Date: 2019/03/26 14:28
- Name: Naoya Yamaguchi
- Hi,
Your problem seems the same as the following:
http://www.openmx-square.org/forum/patio.cgi?mode=view&no=2421
And, the solution is to use OpenMX 3.8.4 or to copy "MD_pac.c" from OpenMX 3.8.4 to OpenMX 3.8.5.
Regards,
Naoya Yamaguchi
|
| Re: The problem of RF constrained optimization with patch 3.8.4 and 3.8.5 ( No.3 ) |
- Date: 2019/03/26 22:42
- Name: Alisa
- Hi,
I copied the "MD_pac.c" from patch 3.8.4 to patch 3.8.5 and reinstalled openmx3.8,but the following waring message appeared.
mpicc -O3 -Dscalapack -ffast-math -fopenmp -I/opt/intel/composer_xe_2015.1.133/mkl/include/fftw -I/opt/intel/composer_xe_2015.1.133/mkl/include/ -I./liberi-091216/source -c DFTD3vdW_init.c
DFTD3vdW_init.c: In function ‘DFTD3vdW_init’:
DFTD3vdW_init.c:33502:3: warning: incompatible implicit declaration of built-in function ‘memset’ [enabled by default]
memset( maxcn_dftD, -1, sizeof( maxcn_dftD) );
mpicc -O3 -Dscalapack -ffast-math -fopenmp -I/opt/intel/composer_xe_2015.1.133/mkl/include/fftw -I/opt/intel/composer_xe_2015.1.133/mkl/include/ -I./liberi-091216/source -g -c -o exx_rhox.o exx_rhox.c
mpicc -O3 -Dscalapack -ffast-math -fopenmp -I/opt/intel/composer_xe_2015.1.133/mkl/include/fftw -I/opt/intel/composer_xe_2015.1.133/mkl/include/ -I./liberi-091216/source -g -c -o liberi-091216/source/eri.o liberi-091216/source/eri.c
beri-091216/source/eri.c: In function ‘ERI_Overlap’:
liberi-091216/source/eri.c:133:5: warning: passing argument 5 of ‘ERI_LL_Overlap_d’ from incompatible pointer type [enabled by default]
ERI_LL_Overlap_d(solver, p, dp, alp1, dalp1, alp2, dalp2, cx);
^
In file included from liberi-091216/source/eri.c:14:0:
liberi-091216/source/eri.h:527:6: note: expected ‘const double **’ but argument is of type ‘double **’
void ERI_LL_Overlap_d(
^
liberi-091216/source/eri.c:133:5: warning: passing argument 7 of ‘ERI_LL_Overlap_d’ from incompatible pointer type [enabled by default]
ERI_LL_Overlap_d(solver, p, dp, alp1, dalp1, alp2, dalp2, cx);
^
In file included from liberi-091216/source/eri.c:14:0:
liberi-091216/source/eri.h:527:6: note: expected ‘const double **’ but argument is of type ‘double **’
void ERI_LL_Overlap_d(
^
liberi-091216/source/eri.c: In function ‘ERI_Integral’:
liberi-091216/source/eri.c:229:23: warning: passing argument 3 of ‘ERI_Integral_GL_d’ from incompatible pointer type [enabled by default]
R[0], R[1], R[2], cx12, cx34, 1e-10, scr, lmax_gl);
^
In file included from liberi-091216/source/eri.c:14:0:
liberi-091216/source/eri.h:571:6: note: expected ‘double (*)[3][2]’ but argument is of type ‘double *’
void ERI_Integral_GL_d(
^
liberi-091216/source/eri.c:229:23: warning: passing argument 6 of ‘ERI_Integral_GL_d’ from incompatible pointer type [enabled by default]
R[0], R[1], R[2], cx12, cx34, 1e-10, scr, lmax_gl);
^
In file included from liberi-091216/source/eri.c:14:0:
liberi-091216/source/eri.h:571:6: note: expected ‘const double **’ but argument is of type ‘double **’
void ERI_Integral_GL_d(
^
liberi-091216/source/eri.c:229:23: warning: passing argument 7 of ‘ERI_Integral_GL_d’ from incompatible pointer type [enabled by default]
R[0], R[1], R[2], cx12, cx34, 1e-10, scr, lmax_gl);
^
In file included from liberi-091216/source/eri.c:14:0:
liberi-091216/source/eri.h:571:6: note: expected ‘const double **’ but argument is of type ‘double **’
void ERI_Integral_GL_d(
Thank you!
Alisa
|
| Re: The problem of RF constrained optimization with patch 3.8.4 and 3.8.5 ( No.4 ) |
- Date: 2019/03/27 00:40
- Name: Naoya Yamaguchi
- Dear Alisa,
If there is no error except warning or note messages, and you can find the executable file "openmx", I think your installation succeeded.
You can do test calculations by executing "./openmx -runtest" If you need it as follows:
http://www.openmx-square.org/openmx_man3.8/node20.html
Regards,
Naoya Yamaguchi
|
|
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The problem of RF constrained optimization with patch 3.8.4 and 3.8.5