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siesta-3-serial

mahmoodn
Oct 6th, 2016
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  1. mahmood@cluster:A$ date
  2. Thu Oct 6 20:33:48 IRST 2016
  3. mahmood@cluster:A$ ../sie/siesta < A.fdf
  4. Siesta Version: siesta-3.2-pl-5
  5. Architecture : x86_64-unknown-linux-gnu--unknown
  6. Compiler flags: f95 -g -O2
  7. SERIAL version
  8.  
  9. * Running in serial mode
  10. >> Start of run: 6-OCT-2016 20:33:50
  11.  
  12. ***********************
  13. * WELCOME TO SIESTA *
  14. ***********************
  15.  
  16. reinit: Reading from standard input
  17. ************************** Dump of input data file ****************************
  18. SystemLabel A
  19. NumberOfAtoms 54
  20. NumberOfSpecies 2
  21. %block ChemicalSpeciesLabel
  22. 1 6 C
  23. 2 1 H
  24. %endblock ChemicalSpeciesLabel
  25. PAO.EnergyShift 100 meV
  26. PAO.BasisType split
  27. %block PAO.BasisSizes
  28. C DZP
  29. H DZP
  30. %endblock PAO.BasisSizes
  31. LatticeConstant 1.000 Ang
  32. #kgrid_cutoff 20. Ang
  33. %block kgrid_Monkhorst_Pack
  34. 1 0 0 0.0
  35. 0 1 0 0.0
  36. 0 0 3 0.0
  37. %endblock kgrid_Monkhorst_Pack
  38. # SPIN options
  39. xc.functional GGA # Exchange-correlation functional
  40. xc.authors PBE # Exchange-correlation version
  41. SpinPolarized F # Logical parameters are: yes or no
  42. FixSpin F
  43. TotalSpin 0.0
  44. NonCollinearSpin F # 'T', 'F'
  45. MeshCutoff 200. Ry # Equivalent plane wave cutoff for the grid
  46. # SCF options
  47. DM.Tolerance 4.d-4 # Tolerance in maximum difference between input and output DM
  48. MaxSCFIterations 1000 # Maximum number of SCF iter
  49. DM.UseSaveDM T # to use continuation files
  50. DM.MixingWeight 0.05 # New DM amount for next SCF cycle
  51. DM.NumberPulay 10
  52. DM.MixSCF1 F
  53. DM.PulayOnFile F # Store in memory ('F') or in files ('T')
  54. # NeglNonOverlapInt T # 'F'=do not neglect
  55. SolutionMethod Diagon # OrderN or Diagon
  56. ElectronicTemperature 300 K # Temp. for Fermi smearing
  57. # MD options
  58. MD.TypeOfRun CG # Type of dynamics:
  59. MD.VariableCell F
  60. MD.NumCGsteps 700 # Number of CG steps for coordinate optimization
  61. ZM.UnitsLength Ang #the units of length used during Z-matrix input
  62. ZM.UnitsAngle deg #the units of angles used during Z-matrix input
  63. ZM.ForceTolLength 0.02 eV/Ang #controls the convergence with respect to forces on Z-matrix lengths
  64. ZM.ForceTolAngle 0.00356549 Ry/rad #controls the convergence with respect to forces on Z-matrix angles
  65. ZM.MaxDisplLength 0.1 Ang # controls the maximum change in a Zmatrix length during an optimisation step
  66. ZM.MaxDisplAngle 0.003 rad # controls the maximum change in a Z-matrix angle during an optimisation step
  67. ZM.CalcAllForces T # Default value
  68. AtomicCoordinatesFormat NotScaledCartesianAng
  69. %block LatticeVectors
  70. 10.0 0.0 0.0
  71. 0.0 20.0 0.0
  72. 0.0 0.0 20.0
  73. %endblock LatticeVectors
  74. AtomicCoordinatesFormat NotScaledCartesianAng
  75. %block AtomicCoordinatesAndAtomicSpecies
  76. 5.000000000 7.539607750 4.316560000 1
  77. 5.000000000 10.000609750 4.316560000 1
  78. 5.000000000 12.461612750 4.316560000 1
  79. 5.000000000 5.355612750 4.476490000 2
  80. 5.000000000 14.618759750 4.491990000 2
  81. 5.000000000 6.309106750 5.026990000 1
  82. 5.000000000 8.770108750 5.026990000 1
  83. 5.000000000 11.231112750 5.026990000 1
  84. 5.000000000 13.692112750 5.026990000 1
  85. 5.000000000 6.309106750 6.447850000 1
  86. 5.000000000 8.770108750 6.447850000 1
  87. 5.000000000 11.231112750 6.447850000 1
  88. 5.000000000 13.692112750 6.447850000 1
  89. 5.000000000 14.618759750 6.982850000 2
  90. 5.000000000 5.355612750 6.998350000 2
  91. 5.000000000 7.539607750 7.158280000 1
  92. 5.000000000 10.000609750 7.158280000 1
  93. 5.000000000 12.461612750 7.158280000 1
  94. 5.000000000 7.539607750 8.579140000 1
  95. 5.000000000 10.000609750 8.579140000 1
  96. 5.000000000 12.461612750 8.579140000 1
  97. 5.000000000 5.355612750 8.739070000 2
  98. 5.000000000 14.618759750 8.754570000 2
  99. 5.000000000 6.309106750 9.289570000 1
  100. 5.000000000 8.770108750 9.289570000 1
  101. 5.000000000 11.231112750 9.289570000 1
  102. 5.000000000 13.692112750 9.289570000 1
  103. 5.000000000 6.309106750 10.710430000 1
  104. 5.000000000 8.770108750 10.710430000 1
  105. 5.000000000 11.231112750 10.710430000 1
  106. 5.000000000 13.692112750 10.710430000 1
  107. 5.000000000 14.618759750 11.245430000 2
  108. 5.000000000 5.355612750 11.260930000 2
  109. 5.000000000 7.539607750 11.420860000 1
  110. 5.000000000 10.000609750 11.420860000 1
  111. 5.000000000 12.461612750 11.420860000 1
  112. 5.000000000 7.539607750 12.841720000 1
  113. 5.000000000 10.000609750 12.841720000 1
  114. 5.000000000 12.461612750 12.841720000 1
  115. 5.000000000 5.355612750 13.001650000 2
  116. 5.000000000 14.618759750 13.017150000 2
  117. 5.000000000 6.309106750 13.552150000 1
  118. 5.000000000 8.770108750 13.552150000 1
  119. 5.000000000 11.231112750 13.552150000 1
  120. 5.000000000 13.692112750 13.552150000 1
  121. 5.000000000 6.309106750 14.973010000 1
  122. 5.000000000 8.770108750 14.973010000 1
  123. 5.000000000 11.231112750 14.973010000 1
  124. 5.000000000 13.692112750 14.973010000 1
  125. 5.000000000 14.618759750 15.508010000 2
  126. 5.000000000 5.355612750 15.523510000 2
  127. 5.000000000 7.539607750 15.683440000 1
  128. 5.000000000 10.000609750 15.683440000 1
  129. 5.000000000 12.461612750 15.683440000 1
  130. %endblock AtomicCoordinatesAndAtomicSpecies
  131. WriteWaveFunctions T # coefficients of the wavefunctions in the basis set orbitals expansion
  132. #WaveFuncKPointsScale ReciprocalLatticeVectors
  133. # Output options
  134. WriteCoorInitial T
  135. WriteCoorStep T
  136. WriteCoorXmol T
  137. WriteForces T
  138. WriteEigenvalues F # If .false., it writes them in the file Systemlabel.EIG
  139. WriteMullikenPop 1 # Write Mulliken Population Analysis
  140. #WriteKpoints T
  141. #WriteKbands T
  142. #WriteBands T
  143. WriteMDCoorXmol T
  144. WriteMDhistory T
  145. WriteCoorCerius t
  146. # Options for saving or reading information
  147. MD.UseSaveZM T # Use stored positions and velocities
  148. MD.UseSaveCG T # Use stored positions and velocities
  149. SaveRho T # Write valence pseudocharge at the mesh
  150. SaveDeltaRho T # Write RHOscf-RHOatm at the mesh
  151. SaveElectrostaticPotential T # Write the total elect. pot. at the mesh
  152. # (local pseudopotential + Hartree)
  153. SaveTotalPotential T # write the valence total effective local potential
  154. # (local pseudopotential + Hartree + Vxc)
  155. WriteSiestaDim T # Write minimum dim to siesta.h and stop
  156. WriteDenchar T # Write information for DENCHAR
  157. %block ProjectedDensityOfStates
  158. -10.00 0.00 0.10 500 eV
  159. %endblock ProjectedDensityOfStates
  160. ************************** End of input data file *****************************
  161.  
  162. reinit: -----------------------------------------------------------------------
  163. reinit: System Name:
  164. reinit: -----------------------------------------------------------------------
  165. reinit: System Label: A
  166. reinit: -----------------------------------------------------------------------
  167.  
  168. initatom: Reading input for the pseudopotentials and atomic orbitals ----------
  169. Species number: 1 Label: C Atomic number: 6
  170. Species number: 2 Label: H Atomic number: 1
  171. Ground state valence configuration: 2s02 2p02
  172. Reading pseudopotential information in formatted form from C.psf
  173.  
  174. Valence configuration for pseudopotential generation:
  175. 2s( 2.00) rc: 1.54
  176. 2p( 2.00) rc: 1.54
  177. 3d( 0.00) rc: 1.54
  178. 4f( 0.00) rc: 1.54
  179. Ground state valence configuration: 1s01
  180. Reading pseudopotential information in formatted form from H.psf
  181.  
  182. Valence configuration for pseudopotential generation:
  183. 1s( 1.00) rc: 1.31
  184. 2p( 0.00) rc: 1.31
  185. 3d( 0.00) rc: 0.37
  186. 4f( 0.00) rc: 1.31
  187. resizes: Read basis size for species C = dzp
  188. resizes: Read basis size for species H = dzp
  189. For C, standard SIESTA heuristics set lmxkb to 3
  190. (one more than the basis l, including polarization orbitals).
  191. Use PS.lmax or PS.KBprojectors blocks to override.
  192. For H, standard SIESTA heuristics set lmxkb to 2
  193. (one more than the basis l, including polarization orbitals).
  194. Use PS.lmax or PS.KBprojectors blocks to override.
  195.  
  196. <basis_specs>
  197. ===============================================================================
  198. C Z= 6 Mass= 12.010 Charge= 0.17977+309
  199. Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
  200. L=0 Nsemic=0 Cnfigmx=2
  201. n=1 nzeta=2 polorb=0
  202. splnorm: 0.15000
  203. vcte: 0.0000
  204. rinn: 0.0000
  205. rcs: 0.0000 0.0000
  206. lambdas: 1.0000 1.0000
  207. L=1 Nsemic=0 Cnfigmx=2
  208. n=1 nzeta=2 polorb=1
  209. splnorm: 0.15000
  210. vcte: 0.0000
  211. rinn: 0.0000
  212. rcs: 0.0000 0.0000
  213. lambdas: 1.0000 1.0000
  214. -------------------------------------------------------------------------------
  215. L=0 Nkbl=1 erefs: 0.17977+309
  216. L=1 Nkbl=1 erefs: 0.17977+309
  217. L=2 Nkbl=1 erefs: 0.17977+309
  218. L=3 Nkbl=1 erefs: 0.17977+309
  219. ===============================================================================
  220. </basis_specs>
  221.  
  222. atom: Called for C (Z = 6)
  223.  
  224. read_vps: Pseudopotential generation method:
  225. read_vps: ATM3 Troullier-Martins
  226. Total valence charge: 4.00000
  227.  
  228. read_vps: Pseudopotential includes a core correction:
  229. read_vps: Pseudo-core for xc-correction
  230.  
  231. xc_check: Exchange-correlation functional:
  232. xc_check: GGA Perdew, Burke & Ernzerhof 1996
  233. V l=0 = -2*Zval/r beyond r= 1.5227
  234. V l=1 = -2*Zval/r beyond r= 1.5227
  235. V l=2 = -2*Zval/r beyond r= 1.5227
  236. V l=3 = -2*Zval/r beyond r= 1.5038
  237. All V_l potentials equal beyond r= 1.5227
  238. This should be close to max(r_c) in ps generation
  239. All pots = -2*Zval/r beyond r= 1.5227
  240.  
  241. VLOCAL1: 99.0% of the norm of Vloc inside 18.722 Ry
  242. VLOCAL1: 99.9% of the norm of Vloc inside 42.668 Ry
  243. atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.83678
  244. atom: Maximum radius for r*vlocal+2*Zval: 1.58088
  245. GHOST: No ghost state for L = 0
  246. GHOST: No ghost state for L = 1
  247. GHOST: No ghost state for L = 2
  248. GHOST: No ghost state for L = 3
  249.  
  250. KBgen: Kleinman-Bylander projectors:
  251. l= 0 rc= 1.704034 el= -1.009801 Ekb= 5.335044 kbcos= 0.316824
  252. l= 1 rc= 1.704034 el= -0.388707 Ekb= -3.785862 kbcos= -0.366464
  253. l= 2 rc= 1.791422 el= 0.001971 Ekb= -0.970471 kbcos= -0.009212
  254. l= 3 rc= 1.859892 el= 0.003065 Ekb= -0.399525 kbcos= -0.001223
  255.  
  256. KBgen: Total number of Kleinman-Bylander projectors: 16
  257. atom: -------------------------------------------------------------------------
  258.  
  259. atom: SANKEY-TYPE ORBITALS:
  260. atom: Selected multiple-zeta basis: split
  261.  
  262. SPLIT: Orbitals with angular momentum L= 0
  263.  
  264. SPLIT: Basis orbitals for state 2s
  265.  
  266. SPLIT: PAO cut-off radius determined from an
  267. SPLIT: energy shift= 0.007350 Ry
  268.  
  269. izeta = 1
  270. lambda = 1.000000
  271. rc = 4.632753
  272. energy = -1.002270
  273. kinetic = 0.855760
  274. potential(screened) = -1.858031
  275. potential(ionic) = -5.417575
  276.  
  277. izeta = 2
  278. rmatch = 3.431921
  279. splitnorm = 0.150000
  280. energy = -0.867111
  281. kinetic = 1.300804
  282. potential(screened) = -2.167915
  283. potential(ionic) = -5.962684
  284.  
  285. SPLIT: Orbitals with angular momentum L= 1
  286.  
  287. SPLIT: Basis orbitals for state 2p
  288.  
  289. SPLIT: PAO cut-off radius determined from an
  290. SPLIT: energy shift= 0.007350 Ry
  291.  
  292. izeta = 1
  293. lambda = 1.000000
  294. rc = 5.658549
  295. energy = -0.381140
  296. kinetic = 2.399701
  297. potential(screened) = -2.780841
  298. potential(ionic) = -6.206085
  299.  
  300. izeta = 2
  301. rmatch = 3.653288
  302. splitnorm = 0.150000
  303. energy = -0.249149
  304. kinetic = 3.542762
  305. potential(screened) = -3.791911
  306. potential(ionic) = -7.581078
  307.  
  308. POLgen: Perturbative polarization orbital with L= 2
  309.  
  310. POLgen: Polarization orbital for state 2p
  311.  
  312. izeta = 1
  313. rc = 5.658549
  314. energy = 1.109913
  315. kinetic = 2.304789
  316. potential(screened) = -1.194876
  317. potential(ionic) = -4.013592
  318. atom: Total number of Sankey-type orbitals: 13
  319.  
  320. atm_pop: Valence configuration (for local Pseudopot. screening):
  321. 2s( 2.00)
  322. 2p( 2.00)
  323. Vna: chval, zval: 4.00000 4.00000
  324.  
  325. Vna: Cut-off radius for the neutral-atom potential: 5.658549
  326. comcore: Pseudo-core radius Rcore= 1.791422
  327.  
  328. atom: _________________________________________________________________________
  329.  
  330. <basis_specs>
  331. ===============================================================================
  332. H Z= 1 Mass= 1.0100 Charge= 0.17977+309
  333. Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
  334. L=0 Nsemic=0 Cnfigmx=1
  335. n=1 nzeta=2 polorb=1
  336. splnorm: 0.15000
  337. vcte: 0.0000
  338. rinn: 0.0000
  339. rcs: 0.0000 0.0000
  340. lambdas: 1.0000 1.0000
  341. -------------------------------------------------------------------------------
  342. L=0 Nkbl=1 erefs: 0.17977+309
  343. L=1 Nkbl=1 erefs: 0.17977+309
  344. L=2 Nkbl=1 erefs: 0.17977+309
  345. ===============================================================================
  346. </basis_specs>
  347.  
  348. atom: Called for H (Z = 1)
  349.  
  350. read_vps: Pseudopotential generation method:
  351. read_vps: ATM3 Troullier-Martins
  352. Total valence charge: 1.00000
  353.  
  354. xc_check: Exchange-correlation functional:
  355. xc_check: GGA Perdew, Burke & Ernzerhof 1996
  356. V l=0 = -2*Zval/r beyond r= 1.2977
  357. V l=1 = -2*Zval/r beyond r= 1.2815
  358. V l=2 = -2*Zval/r beyond r= 1.2656
  359. All V_l potentials equal beyond r= 1.2977
  360. This should be close to max(r_c) in ps generation
  361. All pots = -2*Zval/r beyond r= 1.2977
  362.  
  363. VLOCAL1: 99.0% of the norm of Vloc inside 25.776 Ry
  364. VLOCAL1: 99.9% of the norm of Vloc inside 58.745 Ry
  365. atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.52711
  366. atom: Maximum radius for r*vlocal+2*Zval: 1.28155
  367. GHOST: No ghost state for L = 0
  368. GHOST: No ghost state for L = 1
  369. GHOST: No ghost state for L = 2
  370.  
  371. KBgen: Kleinman-Bylander projectors:
  372. l= 0 rc= 1.434438 el= -0.477200 Ekb= -1.957043 kbcos= -0.361614
  373. l= 1 rc= 1.508111 el= 0.001076 Ekb= -0.424224 kbcos= -0.025441
  374. l= 2 rc= 1.527112 el= 0.002010 Ekb= -0.378578 kbcos= -0.002010
  375.  
  376. KBgen: Total number of Kleinman-Bylander projectors: 9
  377. atom: -------------------------------------------------------------------------
  378.  
  379. atom: SANKEY-TYPE ORBITALS:
  380. atom: Selected multiple-zeta basis: split
  381.  
  382. SPLIT: Orbitals with angular momentum L= 0
  383.  
  384. SPLIT: Basis orbitals for state 1s
  385.  
  386. SPLIT: PAO cut-off radius determined from an
  387. SPLIT: energy shift= 0.007350 Ry
  388.  
  389. izeta = 1
  390. lambda = 1.000000
  391. rc = 5.471469
  392. energy = -0.469871
  393. kinetic = 0.914968
  394. potential(screened) = -1.384840
  395. potential(ionic) = -1.907761
  396.  
  397. izeta = 2
  398. rmatch = 3.952598
  399. splitnorm = 0.150000
  400. energy = -0.377108
  401. kinetic = 1.448266
  402. potential(screened) = -1.825374
  403. potential(ionic) = -2.372743
  404.  
  405. POLgen: Perturbative polarization orbital with L= 1
  406.  
  407. POLgen: Polarization orbital for state 1s
  408.  
  409. izeta = 1
  410. rc = 5.471469
  411. energy = 0.628222
  412. kinetic = 1.275876
  413. potential(screened) = -0.647654
  414. potential(ionic) = -1.125590
  415. atom: Total number of Sankey-type orbitals: 5
  416.  
  417. atm_pop: Valence configuration (for local Pseudopot. screening):
  418. 1s( 1.00)
  419. Vna: chval, zval: 1.00000 1.00000
  420.  
  421. Vna: Cut-off radius for the neutral-atom potential: 5.471469
  422.  
  423. atom: _________________________________________________________________________
  424.  
  425. prinput: Basis input ----------------------------------------------------------
  426.  
  427. PAO.BasisType split
  428.  
  429. %block ChemicalSpeciesLabel
  430. 1 6 C # Species index, atomic number, species label
  431. 2 1 H # Species index, atomic number, species label
  432. %endblock ChemicalSpeciesLabel
  433.  
  434. %block PAO.Basis # Define Basis set
  435. C 2 # Species label, number of l-shells
  436. n=2 0 2 # n, l, Nzeta
  437. 4.633 3.432
  438. 1.000 1.000
  439. n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
  440. 5.659 3.653
  441. 1.000 1.000
  442. H 1 # Species label, number of l-shells
  443. n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
  444. 5.471 3.953
  445. 1.000 1.000
  446. %endblock PAO.Basis
  447.  
  448. prinput: ----------------------------------------------------------------------
  449.  
  450. coor: Atomic-coordinates input format = Cartesian coordinates
  451. coor: (in Angstroms)
  452.  
  453. siesta: Atomic coordinates (Bohr) and species
  454. siesta: 9.44863 14.24780 8.15712 1 1
  455. siesta: 9.44863 18.89842 8.15712 1 2
  456. siesta: 9.44863 23.54904 8.15712 1 3
  457. siesta: 9.44863 10.12065 8.45934 2 4
  458. siesta: 9.44863 27.62546 8.48863 2 5
  459. siesta: 9.44863 11.92249 9.49964 1 6
  460. siesta: 9.44863 16.57311 9.49964 1 7
  461. siesta: 9.44863 21.22374 9.49964 1 8
  462. siesta: 9.44863 25.87435 9.49964 1 9
  463. siesta: 9.44863 11.92249 12.18468 1 10
  464. siesta: 9.44863 16.57311 12.18468 1 11
  465. siesta: 9.44863 21.22374 12.18468 1 12
  466. siesta: 9.44863 25.87435 12.18468 1 13
  467. siesta: 9.44863 27.62546 13.19568 2 14
  468. siesta: 9.44863 10.12065 13.22497 2 15
  469. siesta: 9.44863 14.24780 13.52719 1 16
  470. siesta: 9.44863 18.89842 13.52719 1 17
  471. siesta: 9.44863 23.54904 13.52719 1 18
  472. siesta: 9.44863 14.24780 16.21223 1 19
  473. siesta: 9.44863 18.89842 16.21223 1 20
  474. siesta: 9.44863 23.54904 16.21223 1 21
  475. siesta: 9.44863 10.12065 16.51446 2 22
  476. siesta: 9.44863 27.62546 16.54375 2 23
  477. siesta: 9.44863 11.92249 17.55475 1 24
  478. siesta: 9.44863 16.57311 17.55475 1 25
  479. siesta: 9.44863 21.22374 17.55475 1 26
  480. siesta: 9.44863 25.87435 17.55475 1 27
  481. siesta: 9.44863 11.92249 20.23979 1 28
  482. siesta: 9.44863 16.57311 20.23979 1 29
  483. siesta: 9.44863 21.22374 20.23979 1 30
  484. siesta: 9.44863 25.87435 20.23979 1 31
  485. siesta: 9.44863 27.62546 21.25079 2 32
  486. siesta: 9.44863 10.12065 21.28008 2 33
  487. siesta: 9.44863 14.24780 21.58231 1 34
  488. siesta: 9.44863 18.89842 21.58231 1 35
  489. siesta: 9.44863 23.54904 21.58231 1 36
  490. siesta: 9.44863 14.24780 24.26734 1 37
  491. siesta: 9.44863 18.89842 24.26734 1 38
  492. siesta: 9.44863 23.54904 24.26734 1 39
  493. siesta: 9.44863 10.12065 24.56957 2 40
  494. siesta: 9.44863 27.62546 24.59886 2 41
  495. siesta: 9.44863 11.92249 25.60986 1 42
  496. siesta: 9.44863 16.57311 25.60986 1 43
  497. siesta: 9.44863 21.22374 25.60986 1 44
  498. siesta: 9.44863 25.87435 25.60986 1 45
  499. siesta: 9.44863 11.92249 28.29490 1 46
  500. siesta: 9.44863 16.57311 28.29490 1 47
  501. siesta: 9.44863 21.22374 28.29490 1 48
  502. siesta: 9.44863 25.87435 28.29490 1 49
  503. siesta: 9.44863 27.62546 29.30590 2 50
  504. siesta: 9.44863 10.12065 29.33519 2 51
  505. siesta: 9.44863 14.24780 29.63742 1 52
  506. siesta: 9.44863 18.89842 29.63742 1 53
  507. siesta: 9.44863 23.54904 29.63742 1 54
  508.  
  509. siesta: System type = molecule
  510.  
  511. initatomlists: Number of atoms, orbitals, and projectors: 54 606 780
  512.  
  513. siesta: ******************** Simulation parameters ****************************
  514. siesta:
  515. siesta: The following are some of the parameters of the simulation.
  516. siesta: A complete list of the parameters used, including default values,
  517. siesta: can be found in file out.fdf
  518. siesta:
  519. redata: Non-Collinear-spin run = F
  520. redata: SpinPolarized (Up/Down) run = F
  521. redata: Number of spin components = 1
  522. redata: Long output = F
  523. redata: Number of Atomic Species = 2
  524. redata: Charge density info will appear in .RHO file
  525. redata: Write Mulliken Pop. = Atomic and Orbital charges
  526. redata: Mesh Cutoff = 200.0000 Ry
  527. redata: Net charge of the system = 0.0000 |e|
  528. redata: Max. number of SCF Iter = 1000
  529. redata: Performing Pulay mixing using = 10 iterations
  530. redata: Mix DM in first SCF step ? = F
  531. redata: Write Pulay info on disk? = F
  532. redata: Discard 1st Pulay DM after kick = F
  533. redata: New DM Mixing Weight = 0.0500
  534. redata: New DM Occupancy tolerance = 0.000000000001
  535. redata: No kicks to SCF
  536. redata: DM Mixing Weight for Kicks = 0.5000
  537. redata: DM Tolerance for SCF = 0.000400
  538. redata: Require Energy convergence for SCF = F
  539. redata: DM Energy tolerance for SCF = 0.000100 eV
  540. redata: Require Harris convergence for SCF = F
  541. redata: DM Harris energy tolerance for SCF = 0.000100 eV
  542. redata: Using Saved Data (generic) = F
  543. redata: Use continuation files for DM = T
  544. redata: Neglect nonoverlap interactions = F
  545. redata: Method of Calculation = Diagonalization
  546. redata: Divide and Conquer = T
  547. redata: Electronic Temperature = 0.0019 Ry
  548. redata: Fix the spin of the system = F
  549. redata: Dynamics option = CG coord. optimization
  550. redata: Variable cell = F
  551. redata: Use continuation files for CG = T
  552. redata: Max atomic displ per move = 0.2000 Bohr
  553. redata: Maximum number of CG moves = 700
  554. redata: Force tolerance = 0.0016 Ry/Bohr
  555. redata: ***********************************************************************
  556. Total number of electrons: 180.000000
  557. Total ionic charge: 180.000000
  558. Kpoints in: 2 . Kpoints trimmed: 2
  559.  
  560. siesta: k-grid: Number of k-points = 2
  561. siesta: k-grid: Cutoff (effective) = 5.000 Ang
  562. siesta: k-grid: Supercell and displacements
  563. siesta: k-grid: 1 0 0 0.000
  564. siesta: k-grid: 0 1 0 0.000
  565. siesta: k-grid: 0 0 3 0.000
  566. Naive supercell factors: 2 1 1
  567.  
  568. superc: Internal auxiliary supercell: 2 x 1 x 1 = 2
  569. superc: Number of atoms, orbitals, and projectors: 108 1212 1560
  570.  
  571. * Maximum dynamic memory allocated = 2 MB
  572.  
  573. siesta: ==============================
  574. Begin CG move = 0
  575. ==============================
  576.  
  577. outcoor: Atomic coordinates (Ang):
  578. 5.00000000 7.53960775 4.31656000 1 1 C
  579. 5.00000000 10.00060975 4.31656000 1 2 C
  580. 5.00000000 12.46161275 4.31656000 1 3 C
  581. 5.00000000 5.35561275 4.47649000 2 4 H
  582. 5.00000000 14.61875975 4.49199000 2 5 H
  583. 5.00000000 6.30910675 5.02699000 1 6 C
  584. 5.00000000 8.77010875 5.02699000 1 7 C
  585. 5.00000000 11.23111275 5.02699000 1 8 C
  586. 5.00000000 13.69211275 5.02699000 1 9 C
  587. 5.00000000 6.30910675 6.44785000 1 10 C
  588. 5.00000000 8.77010875 6.44785000 1 11 C
  589. 5.00000000 11.23111275 6.44785000 1 12 C
  590. 5.00000000 13.69211275 6.44785000 1 13 C
  591. 5.00000000 14.61875975 6.98285000 2 14 H
  592. 5.00000000 5.35561275 6.99835000 2 15 H
  593. 5.00000000 7.53960775 7.15828000 1 16 C
  594. 5.00000000 10.00060975 7.15828000 1 17 C
  595. 5.00000000 12.46161275 7.15828000 1 18 C
  596. 5.00000000 7.53960775 8.57914000 1 19 C
  597. 5.00000000 10.00060975 8.57914000 1 20 C
  598. 5.00000000 12.46161275 8.57914000 1 21 C
  599. 5.00000000 5.35561275 8.73907000 2 22 H
  600. 5.00000000 14.61875975 8.75457000 2 23 H
  601. 5.00000000 6.30910675 9.28957000 1 24 C
  602. 5.00000000 8.77010875 9.28957000 1 25 C
  603. 5.00000000 11.23111275 9.28957000 1 26 C
  604. 5.00000000 13.69211275 9.28957000 1 27 C
  605. 5.00000000 6.30910675 10.71043000 1 28 C
  606. 5.00000000 8.77010875 10.71043000 1 29 C
  607. 5.00000000 11.23111275 10.71043000 1 30 C
  608. 5.00000000 13.69211275 10.71043000 1 31 C
  609. 5.00000000 14.61875975 11.24543000 2 32 H
  610. 5.00000000 5.35561275 11.26093000 2 33 H
  611. 5.00000000 7.53960775 11.42086000 1 34 C
  612. 5.00000000 10.00060975 11.42086000 1 35 C
  613. 5.00000000 12.46161275 11.42086000 1 36 C
  614. 5.00000000 7.53960775 12.84172000 1 37 C
  615. 5.00000000 10.00060975 12.84172000 1 38 C
  616. 5.00000000 12.46161275 12.84172000 1 39 C
  617. 5.00000000 5.35561275 13.00165000 2 40 H
  618. 5.00000000 14.61875975 13.01715000 2 41 H
  619. 5.00000000 6.30910675 13.55215000 1 42 C
  620. 5.00000000 8.77010875 13.55215000 1 43 C
  621. 5.00000000 11.23111275 13.55215000 1 44 C
  622. 5.00000000 13.69211275 13.55215000 1 45 C
  623. 5.00000000 6.30910675 14.97301000 1 46 C
  624. 5.00000000 8.77010875 14.97301000 1 47 C
  625. 5.00000000 11.23111275 14.97301000 1 48 C
  626. 5.00000000 13.69211275 14.97301000 1 49 C
  627. 5.00000000 14.61875975 15.50801000 2 50 H
  628. 5.00000000 5.35561275 15.52351000 2 51 H
  629. 5.00000000 7.53960775 15.68344000 1 52 C
  630. 5.00000000 10.00060975 15.68344000 1 53 C
  631. 5.00000000 12.46161275 15.68344000 1 54 C
  632.  
  633. superc: Internal auxiliary supercell: 2 x 1 x 1 = 2
  634. superc: Number of atoms, orbitals, and projectors: 108 1212 1560
  635.  
  636. outcell: Unit cell vectors (Ang):
  637. 10.000000 0.000000 0.000000
  638. 0.000000 20.000000 0.000000
  639. 0.000000 0.000000 20.000000
  640.  
  641. outcell: Cell vector modules (Ang) : 10.000000 20.000000 20.000000
  642. outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
  643. outcell: Cell volume (Ang**3) : 4000.0000
  644. New_DM. Step: 1
  645. Initializing Density Matrix...
  646.  
  647. InitMesh: MESH = 90 x 180 x 180 = 2916000
  648. InitMesh: Mesh cutoff (required, used) = 200.000 223.865 Ry
  649.  
  650. * Maximum dynamic memory allocated = 363 MB
  651.  
  652. stepf: Fermi-Dirac step function
  653.  
  654. siesta: Program's energy decomposition (eV):
  655. siesta: Ebs = -2764.552497
  656. siesta: Eions = 10960.021970
  657. siesta: Ena = 2402.139500
  658. siesta: Ekin = 3869.988559
  659. siesta: Enl = 66.413028
  660. siesta: DEna = -0.000008
  661. siesta: DUscf = 0.000000
  662. siesta: DUext = 0.000000
  663. siesta: Exc = -2376.340999
  664. siesta: eta*DQ = 0.000000
  665. siesta: Emadel = 0.000000
  666. siesta: Emeta = 0.000000
  667. siesta: Emolmec = 0.000000
  668. siesta: Ekinion = 0.000000
  669. siesta: Eharris = -6997.285168
  670. siesta: Etot = -6997.821891
  671. siesta: FreeEng = -6997.821891
  672.  
  673. siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV)
  674. siesta: 1 -6997.2852 -6997.8219 -6997.8219 1.9478 -7.0550
  675. timer: Routine,Calls,Time,% = IterSCF 1 41.162 97.32
  676. elaps: Routine,Calls,Wall,% = IterSCF 1 88.245 98.73
  677. siesta: 2 -6995.5710 -6979.1304 -6979.2076 1.1332 -3.0040
  678. siesta: 3 -6988.4334 -6984.7326 -6984.7573 0.8727 -3.5989
  679. siesta: 4 -6988.3877 -6984.1706 -6984.2373 0.9974 -3.6240
  680. siesta: 5 -6987.4963 -6984.3120 -6984.3197 0.8479 -3.7722
  681. siesta: 6 -6989.6064 -6983.4914 -6983.5005 0.9377 -3.7433
  682. siesta: 7 -6989.7368 -6983.5914 -6983.5950 0.9438 -3.8114
  683. siesta: 8 -6989.5617 -6983.3162 -6983.3220 1.0130 -4.2295
  684. siesta: 9 -6989.1057 -6983.3055 -6983.3092 0.6526 -4.1951
  685. siesta: 10 -6987.7380 -6983.6310 -6983.6501 1.1446 -4.4989
  686. siesta: 11 -6985.9660 -6983.6660 -6983.6660 0.6916 -4.6073
  687. siesta: 12 -6986.0314 -6983.7028 -6983.7306 0.6918 -4.5761
  688. siesta: 13 -6985.7867 -6984.2148 -6984.2417 0.6244 -4.5442
  689. siesta: 14 -6985.8631 -6984.4144 -6984.4421 0.6860 -4.5003
  690. siesta: 15 -6986.5332 -6985.7475 -6985.7715 0.4947 -4.3396
  691. siesta: 16 -6987.1387 -6986.6318 -6986.6515 1.2129 -4.4570
  692. siesta: 17 -6985.6345 -6984.7151 -6984.7153 0.5210 -4.5470
  693. siesta: 18 -6985.6483 -6984.6991 -6984.7361 0.5439 -4.5495
  694. siesta: 19 -6985.6643 -6984.6744 -6984.7113 0.5714 -4.5571
  695. siesta: 20 -6985.5710 -6984.7380 -6984.7744 0.4909 -4.5627
  696. siesta: 21 -6985.4536 -6984.9508 -6984.9961 0.3452 -4.5589
  697. siesta: 22 -6985.4983 -6984.8858 -6984.9605 0.3111 -4.5938
  698. siesta: 23 -6985.4994 -6984.8765 -6984.9374 0.3309 -4.5808
  699. siesta: 24 -6985.4630 -6984.9673 -6985.0274 0.3605 -4.5691
  700. siesta: 25 -6985.4709 -6984.8944 -6984.9682 0.4198 -4.5718
  701. siesta: 26 -6985.5994 -6984.9023 -6984.9772 0.4844 -4.5809
  702. siesta: 27 -6985.7736 -6984.7111 -6984.7536 0.5681 -4.5390
  703. siesta: 28 -6985.7722 -6984.7118 -6984.7431 0.5679 -4.5415
  704. siesta: 29 -6985.7693 -6984.5999 -6984.6312 0.5676 -4.5211
  705. siesta: 30 -6985.7596 -6984.5913 -6984.6233 0.5880 -4.5384
  706. ^C
  707. mahmood@cluster:A$ date
  708. Thu Oct 6 21:07:18 IRST 2016
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