API tools faq
paste
mahmoodn

siesta-4-mpi-201

mahmoodn
Oct 6th, 2016
388
0
Never
Add comment
Not a member of Pastebin yet? Sign Up, it unlocks many cool features!
text 30.23 KB | None | 0 0
raw download clone embed print report
  1. mahmood@cluster:A$ date
  2. Thu Oct 6 20:33:38 IRST 2016
  3. mahmood@cluster:A$ /share/apps/siesta/openmpi-2.0.1/bin/mpirun --hostfile hosts.txt -np 4 /share/apps/siesta/siesta-4.0-mpi201/spar/siesta < A.fdf
  4. Siesta Version: siesta-4.0--500
  5. Architecture : x86_64-unknown-linux-gnu--unknown
  6. Compiler flags: /share/apps/computer/openmpi-2.0.1/bin/mpifort -g -Os
  7. PP flags : -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
  8. PARALLEL version
  9.  
  10. * Running on 4 nodes in parallel
  11. >> Start of run: 6-OCT-2016 20:33:40
  12.  
  13. ***********************
  14. * WELCOME TO SIESTA *
  15. ***********************
  16.  
  17. reinit: Reading from standard input
  18. ************************** Dump of input data file ****************************
  19. SystemLabel A
  20. NumberOfAtoms 54
  21. NumberOfSpecies 2
  22. %block ChemicalSpeciesLabel
  23. 1 6 C
  24. 2 1 H
  25. %endblock ChemicalSpeciesLabel
  26. PAO.EnergyShift 100 meV
  27. PAO.BasisType split
  28. %block PAO.BasisSizes
  29. C DZP
  30. H DZP
  31. %endblock PAO.BasisSizes
  32. LatticeConstant 1.000 Ang
  33. #kgrid_cutoff 20. Ang
  34. %block kgrid_Monkhorst_Pack
  35. 1 0 0 0.0
  36. 0 1 0 0.0
  37. 0 0 3 0.0
  38. %endblock kgrid_Monkhorst_Pack
  39. # SPIN options
  40. xc.functional GGA # Exchange-correlation functional
  41. xc.authors PBE # Exchange-correlation version
  42. SpinPolarized F # Logical parameters are: yes or no
  43. FixSpin F
  44. TotalSpin 0.0
  45. NonCollinearSpin F # 'T', 'F'
  46. MeshCutoff 200. Ry # Equivalent plane wave cutoff for the grid
  47. # SCF options
  48. DM.Tolerance 4.d-4 # Tolerance in maximum difference between input and output DM
  49. MaxSCFIterations 1000 # Maximum number of SCF iter
  50. DM.UseSaveDM T # to use continuation files
  51. DM.MixingWeight 0.05 # New DM amount for next SCF cycle
  52. DM.NumberPulay 10
  53. DM.MixSCF1 F
  54. DM.PulayOnFile F # Store in memory ('F') or in files ('T')
  55. # NeglNonOverlapInt T # 'F'=do not neglect
  56. SolutionMethod Diagon # OrderN or Diagon
  57. ElectronicTemperature 300 K # Temp. for Fermi smearing
  58. # MD options
  59. MD.TypeOfRun CG # Type of dynamics:
  60. MD.VariableCell F
  61. MD.NumCGsteps 700 # Number of CG steps for coordinate optimization
  62. ZM.UnitsLength Ang #the units of length used during Z-matrix input
  63. ZM.UnitsAngle deg #the units of angles used during Z-matrix input
  64. ZM.ForceTolLength 0.02 eV/Ang #controls the convergence with respect to forces on Z-matrix lengths
  65. ZM.ForceTolAngle 0.00356549 Ry/rad #controls the convergence with respect to forces on Z-matrix angles
  66. ZM.MaxDisplLength 0.1 Ang # controls the maximum change in a Zmatrix length during an optimisation step
  67. ZM.MaxDisplAngle 0.003 rad # controls the maximum change in a Z-matrix angle during an optimisation step
  68. ZM.CalcAllForces T # Default value
  69. AtomicCoordinatesFormat NotScaledCartesianAng
  70. %block LatticeVectors
  71. 10.0 0.0 0.0
  72. 0.0 20.0 0.0
  73. 0.0 0.0 20.0
  74. %endblock LatticeVectors
  75. AtomicCoordinatesFormat NotScaledCartesianAng
  76. %block AtomicCoordinatesAndAtomicSpecies
  77. 5.000000000 7.539607750 4.316560000 1
  78. 5.000000000 10.000609750 4.316560000 1
  79. 5.000000000 12.461612750 4.316560000 1
  80. 5.000000000 5.355612750 4.476490000 2
  81. 5.000000000 14.618759750 4.491990000 2
  82. 5.000000000 6.309106750 5.026990000 1
  83. 5.000000000 8.770108750 5.026990000 1
  84. 5.000000000 11.231112750 5.026990000 1
  85. 5.000000000 13.692112750 5.026990000 1
  86. 5.000000000 6.309106750 6.447850000 1
  87. 5.000000000 8.770108750 6.447850000 1
  88. 5.000000000 11.231112750 6.447850000 1
  89. 5.000000000 13.692112750 6.447850000 1
  90. 5.000000000 14.618759750 6.982850000 2
  91. 5.000000000 5.355612750 6.998350000 2
  92. 5.000000000 7.539607750 7.158280000 1
  93. 5.000000000 10.000609750 7.158280000 1
  94. 5.000000000 12.461612750 7.158280000 1
  95. 5.000000000 7.539607750 8.579140000 1
  96. 5.000000000 10.000609750 8.579140000 1
  97. 5.000000000 12.461612750 8.579140000 1
  98. 5.000000000 5.355612750 8.739070000 2
  99. 5.000000000 14.618759750 8.754570000 2
  100. 5.000000000 6.309106750 9.289570000 1
  101. 5.000000000 8.770108750 9.289570000 1
  102. 5.000000000 11.231112750 9.289570000 1
  103. 5.000000000 13.692112750 9.289570000 1
  104. 5.000000000 6.309106750 10.710430000 1
  105. 5.000000000 8.770108750 10.710430000 1
  106. 5.000000000 11.231112750 10.710430000 1
  107. 5.000000000 13.692112750 10.710430000 1
  108. 5.000000000 14.618759750 11.245430000 2
  109. 5.000000000 5.355612750 11.260930000 2
  110. 5.000000000 7.539607750 11.420860000 1
  111. 5.000000000 10.000609750 11.420860000 1
  112. 5.000000000 12.461612750 11.420860000 1
  113. 5.000000000 7.539607750 12.841720000 1
  114. 5.000000000 10.000609750 12.841720000 1
  115. 5.000000000 12.461612750 12.841720000 1
  116. 5.000000000 5.355612750 13.001650000 2
  117. 5.000000000 14.618759750 13.017150000 2
  118. 5.000000000 6.309106750 13.552150000 1
  119. 5.000000000 8.770108750 13.552150000 1
  120. 5.000000000 11.231112750 13.552150000 1
  121. 5.000000000 13.692112750 13.552150000 1
  122. 5.000000000 6.309106750 14.973010000 1
  123. 5.000000000 8.770108750 14.973010000 1
  124. 5.000000000 11.231112750 14.973010000 1
  125. 5.000000000 13.692112750 14.973010000 1
  126. 5.000000000 14.618759750 15.508010000 2
  127. 5.000000000 5.355612750 15.523510000 2
  128. 5.000000000 7.539607750 15.683440000 1
  129. 5.000000000 10.000609750 15.683440000 1
  130. 5.000000000 12.461612750 15.683440000 1
  131. %endblock AtomicCoordinatesAndAtomicSpecies
  132. WriteWaveFunctions T # coefficients of the wavefunctions in the basis set orbitals expansion
  133. #WaveFuncKPointsScale ReciprocalLatticeVectors
  134. # Output options
  135. WriteCoorInitial T
  136. WriteCoorStep T
  137. WriteCoorXmol T
  138. WriteForces T
  139. WriteEigenvalues F # If .false., it writes them in the file Systemlabel.EIG
  140. WriteMullikenPop 1 # Write Mulliken Population Analysis
  141. #WriteKpoints T
  142. #WriteKbands T
  143. #WriteBands T
  144. WriteMDCoorXmol T
  145. WriteMDhistory T
  146. WriteCoorCerius t
  147. # Options for saving or reading information
  148. MD.UseSaveZM T # Use stored positions and velocities
  149. MD.UseSaveCG T # Use stored positions and velocities
  150. SaveRho T # Write valence pseudocharge at the mesh
  151. SaveDeltaRho T # Write RHOscf-RHOatm at the mesh
  152. SaveElectrostaticPotential T # Write the total elect. pot. at the mesh
  153. # (local pseudopotential + Hartree)
  154. SaveTotalPotential T # write the valence total effective local potential
  155. # (local pseudopotential + Hartree + Vxc)
  156. WriteSiestaDim T # Write minimum dim to siesta.h and stop
  157. WriteDenchar T # Write information for DENCHAR
  158. %block ProjectedDensityOfStates
  159. -10.00 0.00 0.10 500 eV
  160. %endblock ProjectedDensityOfStates
  161. ************************** End of input data file *****************************
  162.  
  163. reinit: -----------------------------------------------------------------------
  164. reinit: System Name:
  165. reinit: -----------------------------------------------------------------------
  166. reinit: System Label: A
  167. reinit: -----------------------------------------------------------------------
  168.  
  169. initatom: Reading input for the pseudopotentials and atomic orbitals ----------
  170. Species number: 1 Label: C Atomic number: 6
  171. Species number: 2 Label: H Atomic number: 1
  172. Ground state valence configuration: 2s02 2p02
  173. Reading pseudopotential information in formatted form from C.psf
  174.  
  175. Valence configuration for pseudopotential generation:
  176. 2s( 2.00) rc: 1.54
  177. 2p( 2.00) rc: 1.54
  178. 3d( 0.00) rc: 1.54
  179. 4f( 0.00) rc: 1.54
  180. Ground state valence configuration: 1s01
  181. Reading pseudopotential information in formatted form from H.psf
  182.  
  183. Valence configuration for pseudopotential generation:
  184. 1s( 1.00) rc: 1.31
  185. 2p( 0.00) rc: 1.31
  186. 3d( 0.00) rc: 0.37
  187. 4f( 0.00) rc: 1.31
  188. resizes: Read basis size for species C = dzp
  189. resizes: Read basis size for species H = dzp
  190. For C, standard SIESTA heuristics set lmxkb to 3
  191. (one more than the basis l, including polarization orbitals).
  192. Use PS.lmax or PS.KBprojectors blocks to override.
  193. For H, standard SIESTA heuristics set lmxkb to 2
  194. (one more than the basis l, including polarization orbitals).
  195. Use PS.lmax or PS.KBprojectors blocks to override.
  196.  
  197. <basis_specs>
  198. ===============================================================================
  199. C Z= 6 Mass= 12.010 Charge= 0.17977+309
  200. Lmxo=1 Lmxkb= 3 BasisType=split Semic=F
  201. L=0 Nsemic=0 Cnfigmx=2
  202. n=1 nzeta=2 polorb=0
  203. splnorm: 0.15000
  204. vcte: 0.0000
  205. rinn: 0.0000
  206. qcoe: 0.0000
  207. qyuk: 0.0000
  208. qwid: 0.10000E-01
  209. rcs: 0.0000 0.0000
  210. lambdas: 1.0000 1.0000
  211. L=1 Nsemic=0 Cnfigmx=2
  212. n=1 nzeta=2 polorb=1
  213. splnorm: 0.15000
  214. vcte: 0.0000
  215. rinn: 0.0000
  216. qcoe: 0.0000
  217. qyuk: 0.0000
  218. qwid: 0.10000E-01
  219. rcs: 0.0000 0.0000
  220. lambdas: 1.0000 1.0000
  221. -------------------------------------------------------------------------------
  222. L=0 Nkbl=1 erefs: 0.17977+309
  223. L=1 Nkbl=1 erefs: 0.17977+309
  224. L=2 Nkbl=1 erefs: 0.17977+309
  225. L=3 Nkbl=1 erefs: 0.17977+309
  226. ===============================================================================
  227. </basis_specs>
  228.  
  229. atom: Called for C (Z = 6)
  230.  
  231. read_vps: Pseudopotential generation method:
  232. read_vps: ATM3 Troullier-Martins
  233. Total valence charge: 4.00000
  234.  
  235. read_vps: Pseudopotential includes a core correction:
  236. read_vps: Pseudo-core for xc-correction
  237.  
  238. xc_check: Exchange-correlation functional:
  239. xc_check: GGA Perdew, Burke & Ernzerhof 1996
  240. V l=0 = -2*Zval/r beyond r= 1.5227
  241. V l=1 = -2*Zval/r beyond r= 1.5227
  242. V l=2 = -2*Zval/r beyond r= 1.5227
  243. V l=3 = -2*Zval/r beyond r= 1.5038
  244. All V_l potentials equal beyond r= 1.5227
  245. This should be close to max(r_c) in ps generation
  246. All pots = -2*Zval/r beyond r= 1.5227
  247.  
  248. VLOCAL1: 99.0% of the norm of Vloc inside 18.722 Ry
  249. VLOCAL1: 99.9% of the norm of Vloc inside 42.668 Ry
  250. atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.83678
  251. atom: Maximum radius for r*vlocal+2*Zval: 1.58088
  252. GHOST: No ghost state for L = 0
  253. GHOST: No ghost state for L = 1
  254. GHOST: No ghost state for L = 2
  255. GHOST: No ghost state for L = 3
  256.  
  257. KBgen: Kleinman-Bylander projectors:
  258. l= 0 rc= 1.704034 el= -1.009801 Ekb= 5.335044 kbcos= 0.316824
  259. l= 1 rc= 1.704034 el= -0.388707 Ekb= -3.785862 kbcos= -0.366464
  260. l= 2 rc= 1.791422 el= 0.001971 Ekb= -0.970471 kbcos= -0.009212
  261. l= 3 rc= 1.859892 el= 0.003065 Ekb= -0.399525 kbcos= -0.001223
  262.  
  263. KBgen: Total number of Kleinman-Bylander projectors: 16
  264. atom: -------------------------------------------------------------------------
  265.  
  266. atom: SANKEY-TYPE ORBITALS:
  267. atom: Selected multiple-zeta basis: split
  268.  
  269. SPLIT: Orbitals with angular momentum L= 0
  270.  
  271. SPLIT: Basis orbitals for state 2s
  272.  
  273. SPLIT: PAO cut-off radius determined from an
  274. SPLIT: energy shift= 0.007350 Ry
  275.  
  276. izeta = 1
  277. lambda = 1.000000
  278. rc = 4.632753
  279. energy = -1.002270
  280. kinetic = 0.855760
  281. potential(screened) = -1.858031
  282. potential(ionic) = -5.417575
  283.  
  284. izeta = 2
  285. rmatch = 3.431921
  286. splitnorm = 0.150000
  287. energy = -0.867111
  288. kinetic = 1.300804
  289. potential(screened) = -2.167915
  290. potential(ionic) = -5.962684
  291.  
  292. SPLIT: Orbitals with angular momentum L= 1
  293.  
  294. SPLIT: Basis orbitals for state 2p
  295.  
  296. SPLIT: PAO cut-off radius determined from an
  297. SPLIT: energy shift= 0.007350 Ry
  298.  
  299. izeta = 1
  300. lambda = 1.000000
  301. rc = 5.658549
  302. energy = -0.381140
  303. kinetic = 2.399701
  304. potential(screened) = -2.780841
  305. potential(ionic) = -6.206085
  306.  
  307. izeta = 2
  308. rmatch = 3.653288
  309. splitnorm = 0.150000
  310. energy = -0.249149
  311. kinetic = 3.542762
  312. potential(screened) = -3.791911
  313. potential(ionic) = -7.581078
  314.  
  315. POLgen: Perturbative polarization orbital with L= 2
  316.  
  317. POLgen: Polarization orbital for state 2p
  318.  
  319. izeta = 1
  320. rc = 5.658549
  321. energy = 1.109913
  322. kinetic = 2.304789
  323. potential(screened) = -1.194876
  324. potential(ionic) = -4.013592
  325. atom: Total number of Sankey-type orbitals: 13
  326.  
  327. atm_pop: Valence configuration (for local Pseudopot. screening):
  328. 2s( 2.00)
  329. 2p( 2.00)
  330. Vna: chval, zval: 4.00000 4.00000
  331.  
  332. Vna: Cut-off radius for the neutral-atom potential: 5.658549
  333. comcore: Pseudo-core radius Rcore= 1.791422
  334.  
  335. atom: _________________________________________________________________________
  336.  
  337. <basis_specs>
  338. ===============================================================================
  339. H Z= 1 Mass= 1.0100 Charge= 0.17977+309
  340. Lmxo=0 Lmxkb= 2 BasisType=split Semic=F
  341. L=0 Nsemic=0 Cnfigmx=1
  342. n=1 nzeta=2 polorb=1
  343. splnorm: 0.15000
  344. vcte: 0.0000
  345. rinn: 0.0000
  346. qcoe: 0.0000
  347. qyuk: 0.0000
  348. qwid: 0.10000E-01
  349. rcs: 0.0000 0.0000
  350. lambdas: 1.0000 1.0000
  351. -------------------------------------------------------------------------------
  352. L=0 Nkbl=1 erefs: 0.17977+309
  353. L=1 Nkbl=1 erefs: 0.17977+309
  354. L=2 Nkbl=1 erefs: 0.17977+309
  355. ===============================================================================
  356. </basis_specs>
  357.  
  358. atom: Called for H (Z = 1)
  359.  
  360. read_vps: Pseudopotential generation method:
  361. read_vps: ATM3 Troullier-Martins
  362. Total valence charge: 1.00000
  363.  
  364. xc_check: Exchange-correlation functional:
  365. xc_check: GGA Perdew, Burke & Ernzerhof 1996
  366. V l=0 = -2*Zval/r beyond r= 1.2977
  367. V l=1 = -2*Zval/r beyond r= 1.2815
  368. V l=2 = -2*Zval/r beyond r= 1.2656
  369. All V_l potentials equal beyond r= 1.2977
  370. This should be close to max(r_c) in ps generation
  371. All pots = -2*Zval/r beyond r= 1.2977
  372.  
  373. VLOCAL1: 99.0% of the norm of Vloc inside 25.776 Ry
  374. VLOCAL1: 99.9% of the norm of Vloc inside 58.745 Ry
  375. atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.52711
  376. atom: Maximum radius for r*vlocal+2*Zval: 1.28155
  377. GHOST: No ghost state for L = 0
  378. GHOST: No ghost state for L = 1
  379. GHOST: No ghost state for L = 2
  380.  
  381. KBgen: Kleinman-Bylander projectors:
  382. l= 0 rc= 1.434438 el= -0.477200 Ekb= -1.957043 kbcos= -0.361614
  383. l= 1 rc= 1.508111 el= 0.001076 Ekb= -0.424224 kbcos= -0.025441
  384. l= 2 rc= 1.527112 el= 0.002010 Ekb= -0.378578 kbcos= -0.002010
  385.  
  386. KBgen: Total number of Kleinman-Bylander projectors: 9
  387. atom: -------------------------------------------------------------------------
  388.  
  389. atom: SANKEY-TYPE ORBITALS:
  390. atom: Selected multiple-zeta basis: split
  391.  
  392. SPLIT: Orbitals with angular momentum L= 0
  393.  
  394. SPLIT: Basis orbitals for state 1s
  395.  
  396. SPLIT: PAO cut-off radius determined from an
  397. SPLIT: energy shift= 0.007350 Ry
  398.  
  399. izeta = 1
  400. lambda = 1.000000
  401. rc = 5.471469
  402. energy = -0.469871
  403. kinetic = 0.914968
  404. potential(screened) = -1.384840
  405. potential(ionic) = -1.907761
  406.  
  407. izeta = 2
  408. rmatch = 3.952598
  409. splitnorm = 0.150000
  410. energy = -0.377108
  411. kinetic = 1.448266
  412. potential(screened) = -1.825374
  413. potential(ionic) = -2.372743
  414.  
  415. POLgen: Perturbative polarization orbital with L= 1
  416.  
  417. POLgen: Polarization orbital for state 1s
  418.  
  419. izeta = 1
  420. rc = 5.471469
  421. energy = 0.628222
  422. kinetic = 1.275876
  423. potential(screened) = -0.647654
  424. potential(ionic) = -1.125590
  425. atom: Total number of Sankey-type orbitals: 5
  426.  
  427. atm_pop: Valence configuration (for local Pseudopot. screening):
  428. 1s( 1.00)
  429. Vna: chval, zval: 1.00000 1.00000
  430.  
  431. Vna: Cut-off radius for the neutral-atom potential: 5.471469
  432.  
  433. atom: _________________________________________________________________________
  434.  
  435. prinput: Basis input ----------------------------------------------------------
  436.  
  437. PAO.BasisType split
  438.  
  439. %block ChemicalSpeciesLabel
  440. 1 6 C # Species index, atomic number, species label
  441. 2 1 H # Species index, atomic number, species label
  442. %endblock ChemicalSpeciesLabel
  443.  
  444. %block PAO.Basis # Define Basis set
  445. C 2 # Species label, number of l-shells
  446. n=2 0 2 # n, l, Nzeta
  447. 4.633 3.432
  448. 1.000 1.000
  449. n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
  450. 5.659 3.653
  451. 1.000 1.000
  452. H 1 # Species label, number of l-shells
  453. n=1 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol
  454. 5.471 3.953
  455. 1.000 1.000
  456. %endblock PAO.Basis
  457.  
  458. prinput: ----------------------------------------------------------------------
  459.  
  460. coor: Atomic-coordinates input format = Cartesian coordinates
  461. coor: (in Angstroms)
  462.  
  463. siesta: Atomic coordinates (Bohr) and species
  464. siesta: 9.44863 14.24780 8.15712 1 1
  465. siesta: 9.44863 18.89842 8.15712 1 2
  466. siesta: 9.44863 23.54904 8.15712 1 3
  467. siesta: 9.44863 10.12065 8.45934 2 4
  468. siesta: 9.44863 27.62546 8.48863 2 5
  469. siesta: 9.44863 11.92249 9.49964 1 6
  470. siesta: 9.44863 16.57311 9.49964 1 7
  471. siesta: 9.44863 21.22374 9.49964 1 8
  472. siesta: 9.44863 25.87435 9.49964 1 9
  473. siesta: 9.44863 11.92249 12.18468 1 10
  474. siesta: 9.44863 16.57311 12.18468 1 11
  475. siesta: 9.44863 21.22374 12.18468 1 12
  476. siesta: 9.44863 25.87435 12.18468 1 13
  477. siesta: 9.44863 27.62546 13.19568 2 14
  478. siesta: 9.44863 10.12065 13.22497 2 15
  479. siesta: 9.44863 14.24780 13.52719 1 16
  480. siesta: 9.44863 18.89842 13.52719 1 17
  481. siesta: 9.44863 23.54904 13.52719 1 18
  482. siesta: 9.44863 14.24780 16.21223 1 19
  483. siesta: 9.44863 18.89842 16.21223 1 20
  484. siesta: 9.44863 23.54904 16.21223 1 21
  485. siesta: 9.44863 10.12065 16.51446 2 22
  486. siesta: 9.44863 27.62546 16.54375 2 23
  487. siesta: 9.44863 11.92249 17.55475 1 24
  488. siesta: 9.44863 16.57311 17.55475 1 25
  489. siesta: 9.44863 21.22374 17.55475 1 26
  490. siesta: 9.44863 25.87435 17.55475 1 27
  491. siesta: 9.44863 11.92249 20.23979 1 28
  492. siesta: 9.44863 16.57311 20.23979 1 29
  493. siesta: 9.44863 21.22374 20.23979 1 30
  494. siesta: 9.44863 25.87435 20.23979 1 31
  495. siesta: 9.44863 27.62546 21.25079 2 32
  496. siesta: 9.44863 10.12065 21.28008 2 33
  497. siesta: 9.44863 14.24780 21.58231 1 34
  498. siesta: 9.44863 18.89842 21.58231 1 35
  499. siesta: 9.44863 23.54904 21.58231 1 36
  500. siesta: 9.44863 14.24780 24.26734 1 37
  501. siesta: 9.44863 18.89842 24.26734 1 38
  502. siesta: 9.44863 23.54904 24.26734 1 39
  503. siesta: 9.44863 10.12065 24.56957 2 40
  504. siesta: 9.44863 27.62546 24.59886 2 41
  505. siesta: 9.44863 11.92249 25.60986 1 42
  506. siesta: 9.44863 16.57311 25.60986 1 43
  507. siesta: 9.44863 21.22374 25.60986 1 44
  508. siesta: 9.44863 25.87435 25.60986 1 45
  509. siesta: 9.44863 11.92249 28.29490 1 46
  510. siesta: 9.44863 16.57311 28.29490 1 47
  511. siesta: 9.44863 21.22374 28.29490 1 48
  512. siesta: 9.44863 25.87435 28.29490 1 49
  513. siesta: 9.44863 27.62546 29.30590 2 50
  514. siesta: 9.44863 10.12065 29.33519 2 51
  515. siesta: 9.44863 14.24780 29.63742 1 52
  516. siesta: 9.44863 18.89842 29.63742 1 53
  517. siesta: 9.44863 23.54904 29.63742 1 54
  518.  
  519. siesta: System type = molecule
  520.  
  521. initatomlists: Number of atoms, orbitals, and projectors: 54 606 780
  522.  
  523. coxmol: Writing XMOL coordinates into file A.xyz
  524.  
  525. siesta: ******************** Simulation parameters ****************************
  526. siesta:
  527. siesta: The following are some of the parameters of the simulation.
  528. siesta: A complete list of the parameters used, including default values,
  529. siesta: can be found in file out.fdf
  530. siesta:
  531. redata: Non-Collinear-spin run = F
  532. redata: SpinPolarized (Up/Down) run = F
  533. redata: Number of spin components = 1
  534. redata: Long output = F
  535. redata: Number of Atomic Species = 2
  536. redata: Charge density info will appear in .RHO file
  537. redata: Write Mulliken Pop. = Atomic and Orbital charges
  538. redata: Mesh Cutoff = 200.0000 Ry
  539. redata: Net charge of the system = 0.0000 |e|
  540. redata: Min. number of SCF Iter = 0
  541. redata: Max. number of SCF Iter = 1000
  542. redata: Mix DM or H after convergence = F
  543. redata: Recompute H after scf cycle = F
  544. redata: Performing Pulay mixing using = 10 iterations
  545. redata: Mix DM in first SCF step ? = F
  546. redata: Write Pulay info on disk? = F
  547. redata: Discard 1st Pulay DM after kick = F
  548. redata: New DM Mixing Weight = 0.0500
  549. redata: New DM Occupancy tolerance = 0.000000000001
  550. redata: No kicks to SCF
  551. redata: DM Mixing Weight for Kicks = 0.5000
  552. redata: DM Tolerance for SCF = 0.000400
  553. redata: Require (free) Energy convergence in SCF = F
  554. redata: DM (free)Energy tolerance for SCF = 0.000010 eV
  555. redata: Require Harris convergence for SCF = F
  556. redata: DM Harris energy tolerance for SCF = 0.000010 eV
  557. redata: Using Saved Data (generic) = F
  558. redata: Use continuation files for DM = T
  559. redata: Neglect nonoverlap interactions = F
  560. redata: Method of Calculation = Diagonalization
  561. redata: Divide and Conquer = T
  562. redata: Electronic Temperature = 0.0019 Ry
  563. redata: Fix the spin of the system = F
  564. redata: Dynamics option = CG coord. optimization
  565. redata: Variable cell = F
  566. redata: Use continuation files for CG = T
  567. redata: Max atomic displ per move = 0.2000 Bohr
  568. redata: Maximum number of CG moves = 700
  569. redata: Force tolerance = 0.0016 Ry/Bohr
  570. redata: ***********************************************************************
  571. Total number of electrons: 180.000000
  572. Total ionic charge: 180.000000
  573.  
  574. * ProcessorY, Blocksize: 2 24
  575.  
  576.  
  577. * Orbital distribution balance (max,min): 168 144
  578.  
  579. Kpoints in: 2 . Kpoints trimmed: 2
  580.  
  581. siesta: k-grid: Number of k-points = 2
  582. siesta: k-grid: Cutoff (effective) = 5.000 Ang
  583. siesta: k-grid: Supercell and displacements
  584. siesta: k-grid: 1 0 0 0.000
  585. siesta: k-grid: 0 1 0 0.000
  586. siesta: k-grid: 0 0 3 0.000
  587. Naive supercell factors: 2 1 1
  588.  
  589. superc: Internal auxiliary supercell: 2 x 1 x 1 = 2
  590. superc: Number of atoms, orbitals, and projectors: 108 1212 1560
  591.  
  592. ====================================
  593. Begin CG opt. move = 0
  594. ====================================
  595.  
  596. outcoor: Atomic coordinates (Ang):
  597. 5.00000000 7.53960775 4.31656000 1 1 C
  598. 5.00000000 10.00060975 4.31656000 1 2 C
  599. 5.00000000 12.46161275 4.31656000 1 3 C
  600. 5.00000000 5.35561275 4.47649000 2 4 H
  601. 5.00000000 14.61875975 4.49199000 2 5 H
  602. 5.00000000 6.30910675 5.02699000 1 6 C
  603. 5.00000000 8.77010875 5.02699000 1 7 C
  604. 5.00000000 11.23111275 5.02699000 1 8 C
  605. 5.00000000 13.69211275 5.02699000 1 9 C
  606. 5.00000000 6.30910675 6.44785000 1 10 C
  607. 5.00000000 8.77010875 6.44785000 1 11 C
  608. 5.00000000 11.23111275 6.44785000 1 12 C
  609. 5.00000000 13.69211275 6.44785000 1 13 C
  610. 5.00000000 14.61875975 6.98285000 2 14 H
  611. 5.00000000 5.35561275 6.99835000 2 15 H
  612. 5.00000000 7.53960775 7.15828000 1 16 C
  613. 5.00000000 10.00060975 7.15828000 1 17 C
  614. 5.00000000 12.46161275 7.15828000 1 18 C
  615. 5.00000000 7.53960775 8.57914000 1 19 C
  616. 5.00000000 10.00060975 8.57914000 1 20 C
  617. 5.00000000 12.46161275 8.57914000 1 21 C
  618. 5.00000000 5.35561275 8.73907000 2 22 H
  619. 5.00000000 14.61875975 8.75457000 2 23 H
  620. 5.00000000 6.30910675 9.28957000 1 24 C
  621. 5.00000000 8.77010875 9.28957000 1 25 C
  622. 5.00000000 11.23111275 9.28957000 1 26 C
  623. 5.00000000 13.69211275 9.28957000 1 27 C
  624. 5.00000000 6.30910675 10.71043000 1 28 C
  625. 5.00000000 8.77010875 10.71043000 1 29 C
  626. 5.00000000 11.23111275 10.71043000 1 30 C
  627. 5.00000000 13.69211275 10.71043000 1 31 C
  628. 5.00000000 14.61875975 11.24543000 2 32 H
  629. 5.00000000 5.35561275 11.26093000 2 33 H
  630. 5.00000000 7.53960775 11.42086000 1 34 C
  631. 5.00000000 10.00060975 11.42086000 1 35 C
  632. 5.00000000 12.46161275 11.42086000 1 36 C
  633. 5.00000000 7.53960775 12.84172000 1 37 C
  634. 5.00000000 10.00060975 12.84172000 1 38 C
  635. 5.00000000 12.46161275 12.84172000 1 39 C
  636. 5.00000000 5.35561275 13.00165000 2 40 H
  637. 5.00000000 14.61875975 13.01715000 2 41 H
  638. 5.00000000 6.30910675 13.55215000 1 42 C
  639. 5.00000000 8.77010875 13.55215000 1 43 C
  640. 5.00000000 11.23111275 13.55215000 1 44 C
  641. 5.00000000 13.69211275 13.55215000 1 45 C
  642. 5.00000000 6.30910675 14.97301000 1 46 C
  643. 5.00000000 8.77010875 14.97301000 1 47 C
  644. 5.00000000 11.23111275 14.97301000 1 48 C
  645. 5.00000000 13.69211275 14.97301000 1 49 C
  646. 5.00000000 14.61875975 15.50801000 2 50 H
  647. 5.00000000 5.35561275 15.52351000 2 51 H
  648. 5.00000000 7.53960775 15.68344000 1 52 C
  649. 5.00000000 10.00060975 15.68344000 1 53 C
  650. 5.00000000 12.46161275 15.68344000 1 54 C
  651.  
  652. superc: Internal auxiliary supercell: 2 x 1 x 1 = 2
  653. superc: Number of atoms, orbitals, and projectors: 108 1212 1560
  654.  
  655. outcell: Unit cell vectors (Ang):
  656. 10.000000 0.000000 0.000000
  657. 0.000000 20.000000 0.000000
  658. 0.000000 0.000000 20.000000
  659.  
  660. outcell: Cell vector modules (Ang) : 10.000000 20.000000 20.000000
  661. outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
  662. outcell: Cell volume (Ang**3) : 4000.0000
  663. New_DM. Step: 1
  664. Initializing Density Matrix...
  665. New grid distribution: 1
  666. 1 1: 45 1: 45 1: 45
  667. 2 1: 45 1: 45 46: 90
  668. 3 1: 45 46: 90 1: 45
  669. 4 1: 45 46: 90 46: 90
  670.  
  671. InitMesh: MESH = 90 x 180 x 180 = 2916000
  672. InitMesh: (bp) = 45 x 90 x 90 = 364500
  673. InitMesh: Mesh cutoff (required, used) = 200.000 223.865 Ry
  674. ExtMesh (bp) on 0 = 101 x 101 x 101 = 1030301
  675. New grid distribution: 2
  676. 1 1: 45 1: 45 1: 45
  677. 2 1: 45 1: 45 46: 90
  678. 3 1: 45 46: 90 1: 45
  679. 4 1: 45 46: 90 46: 90
  680. New grid distribution: 3
  681. 1 1: 45 1: 45 1: 45
  682. 2 1: 45 1: 45 46: 90
  683. 3 1: 45 46: 90 1: 45
  684. 4 1: 45 46: 90 46: 90
  685. Setting up quadratic distribution...
  686. ExtMesh (bp) on 0 = 101 x 101 x 101 = 1030301
  687. PhiOnMesh: Number of (b)points on node 0 = 91125
  688. PhiOnMesh: nlist on node 0 = 1232327
  689.  
  690. stepf: Fermi-Dirac step function
  691. ^Cmahmood@cluster:A$ date
  692. Thu Oct 6 21:07:25 IRST 2016
Add Comment
Please, Sign In to add comment
Public Pastes
We use cookies for various purposes including analytics. By continuing to use Pastebin, you agree to our use of cookies as described in the Cookies Policy.  OK, I Understand
Not a member of Pastebin yet?
Sign Up, it unlocks many cool features!