第一原理分子動力学プログラム STATE Senri Wiki
開始行:
* Hydrogen molecule [#v5e7ae86]
This tutorial explains how to perform the convergence stu...
With the periodic boundary condition, an isolated molecul...
Here, we use a hydrogen atom with the local density appro...
** SCF calculation [#fe79c3b8]
- Input file (nfinp_1)
0 0 0 0 0 0 : H2 molecul...
5.0 10.0 1 2 2 : GMAX GMAXP...
1 0 : NUM_SPACE_...
10.0 10.0 10.0 90.0 90.0 90.0 : A B C ALPH...
1 1 1 1 1 1 : N1 N2 N3 M...
1 0 : NCORD NINV
-0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
1 0.15 1.00794 3 1 0.d0 : IATOMN ALF...
0 0 0 0 0 : ICOND INIP...
0 1 : IPRE IPRI
200 200 0 57200.00 0 : NMD1 NMD2 ...
3 1 : MIX_WAY MI...
0 8 0.7 : STARTING_M...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM...
100.0 4 1 0.10D-08 : DTIO IMDAL...
0.0010 0.50D+03 0 : WIDTH FORC...
ldapw91 1 : XCTYPE NSPIN
1.00 : DESTM
101 : NBZTYP
0 0 0 : DUMMY ...
0 0 0 : DUMMY ...
2 : NEG
1 : NEXTST
0 : DUMMY
2 : IMSD
0 : EVALUATE_E...
0 : NPDOSAO
0 0.0 : SM_N dopping
- Execution
$ mpirun -np 4 ./STATE < nfinp_1 > nfout_1
- Results~
When STATE is executed, the following greeting is printed
*******************************************************...
* ...
* ...
* ...
* ****** ******** ** ******** *****...
* ******** ******** **** ******** *****...
* ** ** ** ** ** ** ...
* *** ** ******** ** *****...
* *** ** ********** ** *****...
* ** ** ** ** ** ** ...
* ******** ** ** ** ** *****...
* ****** ** VERSION 5.6.5 ** *****...
* RICS-AIST ...
* OSAKA UNIVERSITY ...
* ...
*******************************************************...
At the convergence, following total energy and its compon...
TOTAL ENERGY AND ITS COMPONENTS
TOTAL ENERGY = -1.1375878...
FREE ENERGY = -1.1375878...
KINETIC ENERGY = 0.9682457...
HARTREE ENERGY = 0.7357007...
XC ENERGY = -0.6455573...
LOCAL ENERGY = -2.3137234...
NONLOCAL ENERGY = -0.0233694...
EWALD ENERGY = 0.1411159...
PC ENERGY = 0.0000000...
ENTROPIC ENERGY = 0.0000000...
This is followed by the Fermi energy, the Kohn-Sham eigen...
FERMI ENERGY = ...
NKP= 1 NGP= 2103 K=( 0.00000 0.00000 0.000...
EIGEN VALUE
-0.37074 -0.00963
OCCUPATION
1.00000 0.00000
Further, the forces acting on atoms are printed out
ATOM COORDINATES ...
MD: 1
MD: 1 H -0.710000 0.000000 0.000000 -0.012...
MD: 2 H 0.710000 0.000000 0.000000 0.012...
** Convergence study [#l563ddc2]
In a calculation with a plane-wave basis set, kinetic ene...
In the case of the ultrasoft pseudopotentials, cutoff ene...
In the STATE code, cutoff wave vectors in the atomic unit...
GMAX**2 and GMAXP**2 are the cutoff energies in Ry.
By performing the total energy calculation with varying G...
[GMAXP=15 (E_cut^den=225 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12781490
4.5 -1.13418820
5.0 -1.13697688
5.5 -1.13816998
6.0 -1.13847300
6.5 -1.13850127
7.0 -1.13851867
7.5 -1.13857102
[GMAXP=20 (E_cut^den=400 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12780183
4.5 -1.13417130
5.0 -1.13695809
5.5 -1.13815036
6.0 -1.13845313
6.5 -1.13848136
7.0 -1.13849876
7.5 -1.13855109
[GMAXP=25 (E_cut^den=625 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12780130
4.5 -1.13417074
5.0 -1.13695751
5.5 -1.13814979
6.0 -1.13845255
6.5 -1.13848078
7.0 -1.13849818
7.5 -1.13855052
[GMAXP=30 (E_cut^den=900 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12780182
4.5 -1.13417124
5.0 -1.13695801
5.5 -1.13815027
6.0 -1.13845303
6.5 -1.13848127
7.0 -1.13849867
7.5 -1.13855100
With GMAX=6 and GMAXP=20, the total energy converges bett...
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
~
In addition to the cutoff energy, the convergence with re...
#A(Bohr) ETOT(Ha)
5.00 -1.31378028
10.00 -1.13845313
15.00 -1.13662806
20.00 -1.13661187
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
We can see that the cell edge of 10 Bohr is sufficient in...
** Geometry optimization (1) [#le1f0591]
Geometry of a diatomic molecule can be optimized by calcu...
# Bond length (Bohr) Total energy (Hartree)
1.28000000 -1.13291015
1.30000000 -1.13434083
1.32000000 -1.13555229
1.34000000 -1.13655937
1.36000000 -1.13737569
1.38000000 -1.13801370
1.40000000 -1.13848494
1.42000000 -1.13880026
1.44000000 -1.13896985
1.46000000 -1.13900337
1.48000000 -1.13890994
1.50000000 -1.13869810
1.52000000 -1.13837576
1.54000000 -1.13795024
1.56000000 -1.13742831
1.58000000 -1.13681622
1.60000000 -1.13611994
1.62000000 -1.13534513
1.64000000 -1.13449712
1.66000000 -1.13358088
By fitting the total energy to sixth order polynomial, eq...
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
** Geometry optimization (2) [#sd3a20f3]
In a complex system, manual optimization is difficult to ...
In such a case, Hellmann-Feynman forces are used to perfo...
To do so, we set the force criterion (FORCCR) of 1.e-3 to...
Note that for SCF calculation, we set a large FORCCR such...
In this example, generalized direct inversion of iterativ...
0 0 0 0 0 0 : H2 molecul...
6.0 20.0 1 2 2 : GMAX GMAXP...
1 0 : NUM_SPACE_...
10.0 10.0 10.0 90.0 90.0 90.0 : A B C ALPH...
1 1 1 1 1 1 : N1 N2 N3 M...
1 0 : NCORD NINV
-0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
1 0.15 1.00794 3 1 0.d0 : IATOMN ALF...
0 0 0 0 0 : ICOND INIP...
0 1 : IPRE IPRI
200 200 0 57200.00 0 : NMD1 NMD2 ...
3 1 : MIX_WAY MI...
0 8 0.7 : STARTING_M...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM...
100.0 4 1 0.10D-08 : DTIO IMDAL...
0.0010 0.50D-03 0 : WIDTH FORC...
ldapw91 1 : XCTYPE NSPIN
1.00 : DESTM
101 : NBZTYP
0 0 0 : DUMMY
0 0 0 : DUMMY
2 : NEG
1 : NEXTST
0 : DUMMY
2 : IMSD
0 : EVALUATE_E...
0 : NPDOSAO
0 0.0 : SM_N dopping
Calculated equilibrium bond length is 1.455 Bohr (0.77 An...
** Excercise [#k23f33e1]
- Perform the convergence study of bond length with respe...
終了行:
* Hydrogen molecule [#v5e7ae86]
This tutorial explains how to perform the convergence stu...
With the periodic boundary condition, an isolated molecul...
Here, we use a hydrogen atom with the local density appro...
** SCF calculation [#fe79c3b8]
- Input file (nfinp_1)
0 0 0 0 0 0 : H2 molecul...
5.0 10.0 1 2 2 : GMAX GMAXP...
1 0 : NUM_SPACE_...
10.0 10.0 10.0 90.0 90.0 90.0 : A B C ALPH...
1 1 1 1 1 1 : N1 N2 N3 M...
1 0 : NCORD NINV
-0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
1 0.15 1.00794 3 1 0.d0 : IATOMN ALF...
0 0 0 0 0 : ICOND INIP...
0 1 : IPRE IPRI
200 200 0 57200.00 0 : NMD1 NMD2 ...
3 1 : MIX_WAY MI...
0 8 0.7 : STARTING_M...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM...
100.0 4 1 0.10D-08 : DTIO IMDAL...
0.0010 0.50D+03 0 : WIDTH FORC...
ldapw91 1 : XCTYPE NSPIN
1.00 : DESTM
101 : NBZTYP
0 0 0 : DUMMY ...
0 0 0 : DUMMY ...
2 : NEG
1 : NEXTST
0 : DUMMY
2 : IMSD
0 : EVALUATE_E...
0 : NPDOSAO
0 0.0 : SM_N dopping
- Execution
$ mpirun -np 4 ./STATE < nfinp_1 > nfout_1
- Results~
When STATE is executed, the following greeting is printed
*******************************************************...
* ...
* ...
* ...
* ****** ******** ** ******** *****...
* ******** ******** **** ******** *****...
* ** ** ** ** ** ** ...
* *** ** ******** ** *****...
* *** ** ********** ** *****...
* ** ** ** ** ** ** ...
* ******** ** ** ** ** *****...
* ****** ** VERSION 5.6.5 ** *****...
* RICS-AIST ...
* OSAKA UNIVERSITY ...
* ...
*******************************************************...
At the convergence, following total energy and its compon...
TOTAL ENERGY AND ITS COMPONENTS
TOTAL ENERGY = -1.1375878...
FREE ENERGY = -1.1375878...
KINETIC ENERGY = 0.9682457...
HARTREE ENERGY = 0.7357007...
XC ENERGY = -0.6455573...
LOCAL ENERGY = -2.3137234...
NONLOCAL ENERGY = -0.0233694...
EWALD ENERGY = 0.1411159...
PC ENERGY = 0.0000000...
ENTROPIC ENERGY = 0.0000000...
This is followed by the Fermi energy, the Kohn-Sham eigen...
FERMI ENERGY = ...
NKP= 1 NGP= 2103 K=( 0.00000 0.00000 0.000...
EIGEN VALUE
-0.37074 -0.00963
OCCUPATION
1.00000 0.00000
Further, the forces acting on atoms are printed out
ATOM COORDINATES ...
MD: 1
MD: 1 H -0.710000 0.000000 0.000000 -0.012...
MD: 2 H 0.710000 0.000000 0.000000 0.012...
** Convergence study [#l563ddc2]
In a calculation with a plane-wave basis set, kinetic ene...
In the case of the ultrasoft pseudopotentials, cutoff ene...
In the STATE code, cutoff wave vectors in the atomic unit...
GMAX**2 and GMAXP**2 are the cutoff energies in Ry.
By performing the total energy calculation with varying G...
[GMAXP=15 (E_cut^den=225 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12781490
4.5 -1.13418820
5.0 -1.13697688
5.5 -1.13816998
6.0 -1.13847300
6.5 -1.13850127
7.0 -1.13851867
7.5 -1.13857102
[GMAXP=20 (E_cut^den=400 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12780183
4.5 -1.13417130
5.0 -1.13695809
5.5 -1.13815036
6.0 -1.13845313
6.5 -1.13848136
7.0 -1.13849876
7.5 -1.13855109
[GMAXP=25 (E_cut^den=625 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12780130
4.5 -1.13417074
5.0 -1.13695751
5.5 -1.13814979
6.0 -1.13845255
6.5 -1.13848078
7.0 -1.13849818
7.5 -1.13855052
[GMAXP=30 (E_cut^den=900 Ry)]
#GMAX ETOT (Ha)
4.0 -1.12780182
4.5 -1.13417124
5.0 -1.13695801
5.5 -1.13815027
6.0 -1.13845303
6.5 -1.13848127
7.0 -1.13849867
7.5 -1.13855100
With GMAX=6 and GMAXP=20, the total energy converges bett...
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
~
In addition to the cutoff energy, the convergence with re...
#A(Bohr) ETOT(Ha)
5.00 -1.31378028
10.00 -1.13845313
15.00 -1.13662806
20.00 -1.13661187
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
We can see that the cell edge of 10 Bohr is sufficient in...
** Geometry optimization (1) [#le1f0591]
Geometry of a diatomic molecule can be optimized by calcu...
# Bond length (Bohr) Total energy (Hartree)
1.28000000 -1.13291015
1.30000000 -1.13434083
1.32000000 -1.13555229
1.34000000 -1.13655937
1.36000000 -1.13737569
1.38000000 -1.13801370
1.40000000 -1.13848494
1.42000000 -1.13880026
1.44000000 -1.13896985
1.46000000 -1.13900337
1.48000000 -1.13890994
1.50000000 -1.13869810
1.52000000 -1.13837576
1.54000000 -1.13795024
1.56000000 -1.13742831
1.58000000 -1.13681622
1.60000000 -1.13611994
1.62000000 -1.13534513
1.64000000 -1.13449712
1.66000000 -1.13358088
By fitting the total energy to sixth order polynomial, eq...
#ref(http://www-cp.prec.eng.osaka-u.ac.jp/puki_state/grap...
** Geometry optimization (2) [#sd3a20f3]
In a complex system, manual optimization is difficult to ...
In such a case, Hellmann-Feynman forces are used to perfo...
To do so, we set the force criterion (FORCCR) of 1.e-3 to...
Note that for SCF calculation, we set a large FORCCR such...
In this example, generalized direct inversion of iterativ...
0 0 0 0 0 0 : H2 molecul...
6.0 20.0 1 2 2 : GMAX GMAXP...
1 0 : NUM_SPACE_...
10.0 10.0 10.0 90.0 90.0 90.0 : A B C ALPH...
1 1 1 1 1 1 : N1 N2 N3 M...
1 0 : NCORD NINV
-0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
0.710 0.000 0.000 1 1 1 : CPS(1:3) I...
1 0.15 1.00794 3 1 0.d0 : IATOMN ALF...
0 0 0 0 0 : ICOND INIP...
0 1 : IPRE IPRI
200 200 0 57200.00 0 : NMD1 NMD2 ...
3 1 : MIX_WAY MI...
0 8 0.7 : STARTING_M...
0.60 0.50 0.60 0.70 1.00 : DTIM1 DTIM...
100.0 4 1 0.10D-08 : DTIO IMDAL...
0.0010 0.50D-03 0 : WIDTH FORC...
ldapw91 1 : XCTYPE NSPIN
1.00 : DESTM
101 : NBZTYP
0 0 0 : DUMMY
0 0 0 : DUMMY
2 : NEG
1 : NEXTST
0 : DUMMY
2 : IMSD
0 : EVALUATE_E...
0 : NPDOSAO
0 0.0 : SM_N dopping
Calculated equilibrium bond length is 1.455 Bohr (0.77 An...
** Excercise [#k23f33e1]
- Perform the convergence study of bond length with respe...
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