1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
|
=------------------------------------------------------------------------------=
CP: variable-cell Car-Parrinello molecular dynamics
using norm-conserving and ultrasoft Vanderbilt pseudopotentials
Version: 4.1 - Tue Jul 14 08:46:06 CEST 2009
Authors: Alfredo Pasquarello, Kari Laasonen, Andrea Trave, Roberto Car,
Paolo Giannozzi, Nicola Marzari, Carlo Cavazzoni, Guido Chiarotti,
Sandro Scandolo, Paolo Focher, Gerardo Ballabio, and others
=------------------------------------------------------------------------------=
This run was started on: 9:27:27 14Jul2009
Serial Build
Job Title: MD Simulation
Atomic Pseudopotentials Parameters
----------------------------------
Reading pseudopotential for specie # 1 from file :
/scratch_local/acv0/espresso-serial/pseudo/O.pz-rrkjus.UPF
file type is 20: UPF
Reading pseudopotential for specie # 2 from file :
/scratch_local/acv0/espresso-serial/pseudo/Si.pz-vbc.UPF
file type is 20: UPF
Main Simulation Parameters (from input)
---------------------------------------
Restart Mode = 0 reset_counters
Number of MD Steps = 10
Print out every 10 MD Steps
Reads from unit = 92
Writes to unit = 93
MD Simulation time step = 12.00
Electronic fictitious mass (emass) = 700.00
emass cut-off = 3.00
Simulation Cell Parameters (from input)
external pressure = 1.00 [GPa]
wmass (calculated) = 49868.25 [AU]
ibrav = 8
alat = 9.28990000
a1 = 9.28990000 0.00000000 0.00000000
a2 = 0.00000000 16.09066419 0.00000000
a3 = 0.00000000 0.00000000 10.21470954
b1 = 0.10764379 0.00000000 0.00000000
b2 = 0.00000000 0.06214784 0.00000000
b3 = 0.00000000 0.00000000 0.09789804
omega = 1526.90153773
Energy Cut-offs
---------------
Ecutwfc = 20.0 Ry, Ecutrho = 150.0 Ry, Ecuts = 80.0 Ry
Gcutwfc = 6.6 , Gcutrho = 18.1 Gcuts = 13.2
modified kinetic energy functional, with parameters:
ecutz = 150.0000 ecsig = 2.0000 ecfix = 16.00
NOTA BENE: refg, mmx = 0.050000 6000
Eigenvalues calculated without the kinetic term contribution
Orthog. with lagrange multipliers : eps = 0.10E-07, max = 30
Electron dynamics with newton equations
Electron dynamics : the temperature is not controlled
Electronic states
-----------------
Number of Electron = 96, of States = 48
Occupation numbers :
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00
Exchange and correlations functionals
-------------------------------------
Using Local Density Approximation with
Exchange functional: SLATER
Correlation functional: PERDEW AND ZUNGER
Exchange-correlation = SLA PZ NOGX NOGC (1100)
Ions Simulation Parameters
--------------------------
Ions are allowed to move
Ions dynamics with newton equations
the temperature is computed for 54 degrees of freedom
ion dynamics with fricp = 0.0000 and greasp = 1.0000
Ionic position (from input)
sorted by specie, and converted to real a.u. coordinates
Species 1 atoms = 12 mass = 29166.22 (a.u.), 16.00 (amu) rcmax = 1.00 (a.u.)
3.188294 14.832370 1.228830
7.832315 6.787040 1.228830
2.074435 5.995380 4.737583
6.720314 14.042319 4.737583
3.963071 11.269898 7.878606
8.608021 3.222959 7.878606
3.963071 4.819153 9.146251
8.608021 12.864483 9.146251
3.187365 1.256681 5.580296
7.833244 9.302011 5.580296
2.075364 10.092062 2.073586
6.719385 2.046732 2.073586
Species 2 atoms = 6 mass = 51040.88 (a.u.), 28.00 (amu) rcmax = 1.00 (a.u.)
0.288916 8.045330 3.404563
4.933866 0.000000 3.404563
2.133890 12.277174 -0.041880
6.778840 4.231844 -0.041880
2.133890 3.813486 6.852027
6.778840 11.858816 6.852027
Ionic position will be re-read from restart file
All atoms are allowed to move
Ionic temperature control via nose thermostat
ion dynamics with nose` temperature control:
temperature required = 300.00000 (kelvin)
NH chain length = 1
active degrees of freedom = 54
time steps per nose osc. = 516
nose` frequency(es) = 6.667
the requested type of NH chains is 0
total number of thermostats used 1 0 0
ionic degrees of freedom for each chain 54
nose` mass(es) for chain 1 = 99946.828
atom i (in sorted order) is assigned to this thermostat :
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Cell Dynamics Parameters (from STDIN)
-------------------------------------
internal stress tensor calculated
Starting cell generated from CELLDM
Cell parameters will be re-read from restart file
Volume dynamics with newton equations
cell parameters dynamics with nose` temp. control
Constant PRESSURE Molecular dynamics:
External pressure (GPa) = 1.00
Volume mass = 49868.25
cell dynamics with nose` temperature control:
Kinetic energy required = 300.00000 (Kelvin)
time steps per nose osc. = 400
nose` frequency = 8.607 (THz)
nose` mass(es) = 9993.391
Verbosity: iprsta = 1
Simulation dimensions initialization
------------------------------------
unit vectors of full simulation cell
in real space: in reciprocal space (units 2pi/alat):
1 9.2899 0.0000 0.0000 1.0000 0.0000 0.0000
2 0.0000 16.0907 0.0000 0.0000 0.5773 0.0000
3 0.0000 0.0000 10.2147 0.0000 0.0000 0.9095
Stick Mesh
----------
nst = 892, nstw = 120, nsts = 476
PEs n.st n.stw n.sts n.g n.gw n.gs
1 1783 239 951 47285 2305 18431
0 1783 239 951 47285 2305 18431
Real Mesh
---------
Global Dimensions Local Dimensions Processor Grid
.X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z.
40 64 40 40 64 40 1 1 1
Array leading dimensions ( nr1x, nr2x, nr3x ) = 40 64 40
Local number of cell to store the grid ( nnrx ) = 102400
Number of x-y planes for each processors:
nr3l = 40
Smooth Real Mesh
----------------
Global Dimensions Local Dimensions Processor Grid
.X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z.
27 45 30 27 45 30 1 1 1
Array leading dimensions ( nr1x, nr2x, nr3x ) = 27 45 30
Local number of cell to store the grid ( nnrx ) = 36450
Number of x-y planes for each processors:
nr3sl = 30
Small Box Real Mesh
-------------------
Global Dimensions Local Dimensions Processor Grid
.X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z.
16 16 16 16 16 16 1 1 1
Array leading dimensions ( nr1x, nr2x, nr3x ) = 16 16 16
Local number of cell to store the grid ( nnrx ) = 4096
unit vectors of box grid cell
in real space: in reciprocal space:
3.7160 0.0000 0.0000 1.0000 0.0000 0.0000
0.0000 4.0227 0.0000 0.0000 0.9238 0.0000
0.0000 0.0000 4.0859 0.0000 0.0000 0.9095
Reciprocal Space Mesh
---------------------
Large Mesh
PE Global(ngmt) Local(ngm) MaxLocal(ngmx)
1 23643 23643 23643
Smooth Mesh
PE Global(ngst) Local(ngs) MaxLocal(ngsx)
1 9216 9216 9216
Wave function Mesh
PE Global(ngwt) Local(ngw) MaxLocal(ngwx)
1 1153 1153 1153
Small box Mesh
ngb = 948 not distributed to processors
System geometry initialization
------------------------------
Scaled positions from standard input
O 0.343200E+00 0.921800E+00 0.120300E+00
O 0.843100E+00 0.421800E+00 0.120300E+00
O 0.223300E+00 0.372600E+00 0.463800E+00
O 0.723400E+00 0.872700E+00 0.463800E+00
O 0.426600E+00 0.700400E+00 0.771300E+00
O 0.926600E+00 0.200300E+00 0.771300E+00
O 0.426600E+00 0.299500E+00 0.895400E+00
O 0.926600E+00 0.799500E+00 0.895400E+00
O 0.343100E+00 0.781000E-01 0.546300E+00
O 0.843200E+00 0.578100E+00 0.546300E+00
O 0.223400E+00 0.627200E+00 0.203000E+00
O 0.723300E+00 0.127200E+00 0.203000E+00
Si 0.311000E-01 0.500000E+00 0.333300E+00
Si 0.531100E+00 0.000000E+00 0.333300E+00
Si 0.229700E+00 0.763000E+00 -0.410000E-02
Si 0.729700E+00 0.263000E+00 -0.410000E-02
Si 0.229700E+00 0.237000E+00 0.670800E+00
Si 0.729700E+00 0.737000E+00 0.670800E+00
ibrav = 8 cell parameters
9.28990 0.00000 0.00000
0.00000 16.09066 0.00000
0.00000 0.00000 10.21471
Pseudopotentials initialization
-------------------------------
nlinit nh(is), ngb, is, kkbeta, lmaxq = 8 948 1
865 3
qqq
-0.0987 0.4865 0.0000 0.0000
0.4865 -2.1787 0.0000 0.0000
0.0000 0.0000 0.2330 0.2950
0.0000 0.0000 0.2950 0.3737
Common initialization
Specie: 1
1 indv= 1 ang. mom= 0
2 indv= 2 ang. mom= 0
3 indv= 3 ang. mom= 1
4 indv= 3 ang. mom= 1
5 indv= 3 ang. mom= 1
6 indv= 4 ang. mom= 1
7 indv= 4 ang. mom= 1
8 indv= 4 ang. mom= 1
dion
0.4817 -1.2813 0.0000 0.0000
-1.2813 2.3075 0.0000 0.0000
0.0000 0.0000 0.6338 0.8752
0.0000 0.0000 0.8752 1.2039
Specie: 2
1 indv= 1 ang. mom= 0
2 indv= 2 ang. mom= 1
3 indv= 2 ang. mom= 1
4 indv= 2 ang. mom= 1
dion
0.7619 0.0000
0.0000 1.8417
Short Legend and Physical Units in the Output
---------------------------------------------
NFI [int] - step index
EKINC [HARTREE A.U.] - kinetic energy of the fictitious electronic dynamics
TEMPH [K] - Temperature of the fictitious cell dynamics
TEMP [K] - Ionic temperature
ETOT [HARTREE A.U.] - Scf total energy (Kohn-Sham hamiltonian)
ENTHAL [HARTREE A.U.] - Enthalpy ( ETOT + P * V )
ECONS [HARTREE A.U.] - Enthalpy + kinetic energy of ions and cell
ECONT [HARTREE A.U.] - Constant of motion for the CP lagrangian
reading restart file: /scratch_local/acv0/tmp//cp_92.save
restart file read in 0.042 sec.
formf: eself= 210.64152
formf: vps(g=0)= -0.0099256 rhops(g=0)= -0.0039295
formf: sum_g vps(g)= -2.2959144 sum_g rhops(g)= -0.5407261
formf: vps(g=0)= -0.0098400 rhops(g=0)= -0.0026197
formf: sum_g vps(g)= -2.3753533 sum_g rhops(g)= -0.3604841
Delta V(G=0): 0.197519Ry, 5.374775eV
formf: eself= 210.64152
formf: vps(g=0)= -0.0099256 rhops(g=0)= -0.0039295
formf: sum_g vps(g)= -2.2959144 sum_g rhops(g)= -0.5407261
formf: vps(g=0)= -0.0098400 rhops(g=0)= -0.0026197
formf: sum_g vps(g)= -2.3753533 sum_g rhops(g)= -0.3604841
Delta V(G=0): 0.197519Ry, 5.374775eV
nfi ekinc temph tempp etot enthal econs econt vnhh xnhh0 vnhp xnhp0
1 0.00000 0.1 0.0 -211.98210 -211.93020 -211.93020 -211.93020 0.0000 0.0000 0.0000 0.0000
Delta V(G=0): 0.197522Ry, 5.374837eV
2 0.00000 0.9 0.1 -211.98211 -211.93021 -211.93020 -211.93020 0.0000 0.0000 0.0000 -0.0001
Delta V(G=0): 0.197526Ry, 5.374960eV
3 0.00000 2.4 0.2 -211.98214 -211.93025 -211.93020 -211.93020 0.0000 0.0000 0.0000 -0.0002
Delta V(G=0): 0.197533Ry, 5.375143eV
4 0.00000 4.7 0.3 -211.98219 -211.93029 -211.93020 -211.93020 0.0000 -0.0001 0.0000 -0.0004
Delta V(G=0): 0.197542Ry, 5.375387eV
5 0.00001 7.7 0.5 -211.98225 -211.93035 -211.93021 -211.93020 0.0000 -0.0001 0.0000 -0.0007
Delta V(G=0): 0.197553Ry, 5.375691eV
6 0.00001 11.5 0.7 -211.98232 -211.93043 -211.93021 -211.93020 0.0000 -0.0002 0.0000 -0.0011
Delta V(G=0): 0.197566Ry, 5.376056eV
7 0.00002 16.1 0.9 -211.98241 -211.93053 -211.93022 -211.93020 0.0000 -0.0003 0.0000 -0.0016
Delta V(G=0): 0.197582Ry, 5.376485eV
8 0.00002 21.5 1.3 -211.98252 -211.93064 -211.93022 -211.93020 0.0000 -0.0003 0.0000 -0.0021
Delta V(G=0): 0.197600Ry, 5.376978eV
9 0.00002 27.7 1.7 -211.98264 -211.93076 -211.93022 -211.93020 0.0000 -0.0004 -0.0001 -0.0027
* Physical Quantities at step: 10
Delta V(G=0): 0.197621Ry, 5.377536eV
10 0.00003 34.8 2.1 -211.98271 -211.93084 -211.93016 -211.93013 0.0000 -0.0005 -0.0001 -0.0033
writing restart file: /scratch_local/acv0/tmp//cp_93.save
restart file written in 0.118 sec.
Averaged Physical Quantities
accomulated this run
ekinc : 0.00001 0.00001 (AU)
ekin : 94.60238 94.60238 (AU)
epot : -343.05127 -343.05127 (AU)
total energy : -211.98234 -211.98234 (AU)
temperature : 0.75835 0.75835 (K )
enthalpy : -211.93045 -211.93045 (AU)
econs : -211.93020 -211.93020 (AU)
pressure : -2.19645 -2.19645 (Gpa)
volume : 1526.61474 1526.61474 (AU)
initialize : 6.93s CPU
total_time : 7.95s CPU ( 10 calls, 0.795 s avg)
formf : 0.47s CPU ( 11 calls, 0.043 s avg)
rhoofr : 2.88s CPU ( 10 calls, 0.288 s avg)
vofrho : 0.72s CPU ( 10 calls, 0.072 s avg)
dforce : 1.27s CPU ( 240 calls, 0.005 s avg)
calphi : 0.07s CPU ( 10 calls, 0.007 s avg)
ortho : 0.33s CPU ( 10 calls, 0.033 s avg)
ortho_iter : 0.03s CPU ( 10 calls, 0.003 s avg)
rsg : 0.01s CPU ( 10 calls, 0.001 s avg)
rhoset : 0.04s CPU ( 10 calls, 0.004 s avg)
updatc : 0.03s CPU ( 10 calls, 0.003 s avg)
newd : 0.78s CPU ( 10 calls, 0.078 s avg)
calbec : 0.04s CPU ( 11 calls, 0.004 s avg)
prefor : 0.03s CPU ( 21 calls, 0.001 s avg)
strucf : 0.02s CPU ( 11 calls, 0.002 s avg)
nlfl : 0.01s CPU ( 10 calls, 0.001 s avg)
nlfq : 0.38s CPU ( 10 calls, 0.038 s avg)
rhov : 0.19s CPU ( 10 calls, 0.019 s avg)
nlsm1 : 0.23s CPU ( 31 calls, 0.007 s avg)
nlsm2 : 0.37s CPU ( 10 calls, 0.037 s avg)
fft : 1.54s CPU ( 130 calls, 0.012 s avg)
ffts : 0.04s CPU ( 20 calls, 0.002 s avg)
fftw : 0.96s CPU ( 720 calls, 0.001 s avg)
fftb : 0.24s CPU ( 2940 calls, 0.000 s avg)
CP : 14.99s CPU time, 15.73s wall time
This run was terminated on: 9:27:43 14Jul2009
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
|
