# -*-shell-script-*-
# Si(1-x) Ge(x) alloy lattice constant and cohesive energy
#setnolog
setoverwrite
dirname = runs/sige-meam
#------------------------------------------------------------
#Read in MEAM potential
meamfile = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meamf"
meafile  = "/home/caiwei/Codes/MD++/Fortran/MEAM-Baskes/meafile_Si_Ge"
ntypes = 2  ename0 = "Siz  " ename1 = "Ge   " #leave spaces to be compatible with fortran
rcut = 6.0  kode0 = "library"
readMEAM
#
#------------------------------------------------------------
# Create Perfect Lattice Configuration
#
latticestructure = diamond-cubic
#latticeconst = 5.5379 #(A) for Ge
latticeconst = 1
makecnspec = [ 1 0 0  4
               0 1 0  4
               0 0 1  4 ]
nspecies = 2 
makecrystal

#Conjugate-Gradient relaxation
conj_ftol = 1e-6 conj_fevalmax = 1000  conj_fixbox = 1

input = [ 288  # number produced by rand_alloy.m (using randperm in Matlab)
  112   275   346   338     3   298    46   292    23   311   495   113   108   322   368   344   326   460   126   300    92   288   276   155   441   412   321   434   317   375   381   202 
  484   194   247    63   447   511   499   257   339   299   433   430   406    18   175    30   482    93   324    25   358   284    71    49   376   466   222   204   343   494   152    45 
  244   110   504   332   111   372   294   415   340   448   295   150    14   417    82   187   124   392   121    76   196    47   177   310    17    72    68   238    32   410   421   269 
   60   186   396   229    31   342   116   272    84   190   185    42   148     6   473   510    66   103   349   184   479   323   480   158   478   211   166   389   192    33   217   314 
  409   408   459   309   443   176    43   130   301   490   405   114   386   249   134    53   378   290   212   440   390   365   313    90   395    24   477   241   216    64   333     8 
  374   140    11   277   143   264    77   234   255   436   205   341   302   435    50   137   325   403   183   267    22   226   367   382   210   208   245   450   383   427   457    12 
  119   420   231   281    54   165   345   107    81    20   230   485   354   388     5   455   115   232   364   472   282   469   132    95     1   356    39   141   278    41   125   353 
  464   173    78   136   219    29    91   279     0   117    56    89    96    21   287   153    73   337   266    99   233   118   402   439    48   399    87   133   195    61   156   369 
  128   362   503   424   250   163   366   161   387   413   178   285   203   199    52   221    37   261    19    51   265   191   160   268   445   489   131   416     2   318   442   461 
  307   296   444    85   425    40   385   315   400   330   423    10   488   452   429   223   467    16   200    88   347   215   291   437   474    27   122   227   220   252   308   123 
   59   352   438   172    75   351   224   384   428   361    58   236   170    65   198   486   240   179   101     7   476   188   228   508   139    79   475   159   242    28   144   470 
  509   293   146   149   237   286   371   253   377   262   401   225   235   256   259   251   492   320   207   379   496   289   458    98   404   127   248   502   491   147   193    34 
  106   263   373   468   283   120   329   243    74   138   357   463   487   297   497   312   145   213   304   162   206   174   306   169    36   370   164   182    13   355   481   336 
  335   167   218   104   507   465   271   483   171   456   100   398   419   471   316   328    80    62   102   397   391   454    35   209   180    15    69     4   446   462   453   258 
   67   331   246   426   260    97   359   157   500    94   363    83   214   142   501   505   129   493   303   360   254   239   189   105   348   109   168   506    44   350   197   280 
    9   380   181   274    26   411   407   498   270   154    38   414   319   305   151   334   393    70   394   451   418    86   273    57   327   135   432   449    55   431   201   422 
]
fixatoms_by_ID input = 1 setfixedatomsspecies freeallatoms saveH

#restoreH input = 5.440 scaleH refreshnnlist relax eval
#restoreH input = 5.441 scaleH refreshnnlist relax eval
#restoreH input = 5.442 scaleH refreshnnlist relax eval
#restoreH input = 5.443 scaleH refreshnnlist relax eval
#restoreH input = 5.444 scaleH refreshnnlist relax eval
#restoreH input = 5.445 scaleH refreshnnlist relax eval
#restoreH input = 5.446 scaleH refreshnnlist relax eval
#restoreH input = 5.447 scaleH refreshnnlist relax eval
#restoreH input = 5.448 scaleH refreshnnlist relax eval
#restoreH input = 5.449 scaleH refreshnnlist relax eval
#restoreH input = 5.450 scaleH refreshnnlist relax eval
#restoreH input = 5.451 scaleH refreshnnlist relax eval
#restoreH input = 5.452 scaleH refreshnnlist relax eval
#restoreH input = 5.453 scaleH refreshnnlist relax eval
#restoreH input = 5.454 scaleH refreshnnlist relax eval
#restoreH input = 5.455 scaleH refreshnnlist relax eval
#restoreH input = 5.456 scaleH refreshnnlist relax eval
#restoreH input = 5.457 scaleH refreshnnlist relax eval
#restoreH input = 5.458 scaleH refreshnnlist relax eval
#restoreH input = 5.459 scaleH refreshnnlist relax eval
#restoreH input = 5.460 scaleH refreshnnlist relax eval
#restoreH input = 5.461 scaleH refreshnnlist relax eval
#restoreH input = 5.462 scaleH refreshnnlist relax eval
#restoreH input = 5.463 scaleH refreshnnlist relax eval
#restoreH input = 5.464 scaleH refreshnnlist relax eval
#restoreH input = 5.465 scaleH refreshnnlist relax eval
#restoreH input = 5.466 scaleH refreshnnlist relax eval
#restoreH input = 5.467 scaleH refreshnnlist relax eval
#restoreH input = 5.468 scaleH refreshnnlist relax eval
#restoreH input = 5.469 scaleH refreshnnlist relax eval
#restoreH input = 5.470 scaleH refreshnnlist relax eval
#restoreH input = 5.471 scaleH refreshnnlist relax eval
#restoreH input = 5.472 scaleH refreshnnlist relax eval
#restoreH input = 5.473 scaleH refreshnnlist relax eval
#restoreH input = 5.474 scaleH refreshnnlist relax eval
#restoreH input = 5.475 scaleH refreshnnlist relax eval
#restoreH input = 5.476 scaleH refreshnnlist relax eval
#restoreH input = 5.477 scaleH refreshnnlist relax eval
#restoreH input = 5.478 scaleH refreshnnlist relax eval
#restoreH input = 5.479 scaleH refreshnnlist relax eval
#restoreH input = 5.480 scaleH refreshnnlist relax eval
#restoreH input = 5.481 scaleH refreshnnlist relax eval
#restoreH input = 5.482 scaleH refreshnnlist relax eval
#restoreH input = 5.483 scaleH refreshnnlist relax eval
#restoreH input = 5.484 scaleH refreshnnlist relax eval
#restoreH input = 5.485 scaleH refreshnnlist relax eval
#restoreH input = 5.486 scaleH refreshnnlist relax eval
#restoreH input = 5.487 scaleH refreshnnlist relax eval
#restoreH input = 5.488 scaleH refreshnnlist relax eval
#restoreH input = 5.489 scaleH refreshnnlist relax eval
#restoreH input = 5.490 scaleH refreshnnlist relax eval
#restoreH input = 5.491 scaleH refreshnnlist relax eval
#restoreH input = 5.492 scaleH refreshnnlist relax eval
#restoreH input = 5.493 scaleH refreshnnlist relax eval
#restoreH input = 5.494 scaleH refreshnnlist relax eval
#restoreH input = 5.495 scaleH refreshnnlist relax eval
#restoreH input = 5.496 scaleH refreshnnlist relax eval
#restoreH input = 5.497 scaleH refreshnnlist relax eval
#restoreH input = 5.498 scaleH refreshnnlist relax eval
#restoreH input = 5.499 scaleH refreshnnlist relax eval
#restoreH input = 5.500 scaleH refreshnnlist relax eval
#restoreH input = 5.501 scaleH refreshnnlist relax eval
#restoreH input = 5.502 scaleH refreshnnlist relax eval
#restoreH input = 5.503 scaleH refreshnnlist relax eval
#restoreH input = 5.504 scaleH refreshnnlist relax eval
#restoreH input = 5.505 scaleH refreshnnlist relax eval
#restoreH input = 5.506 scaleH refreshnnlist relax eval
#restoreH input = 5.507 scaleH refreshnnlist relax eval
#restoreH input = 5.508 scaleH refreshnnlist relax eval
#restoreH input = 5.509 scaleH refreshnnlist relax eval
#restoreH input = 5.510 scaleH refreshnnlist relax eval
#restoreH input = 5.511 scaleH refreshnnlist relax eval
#restoreH input = 5.512 scaleH refreshnnlist relax eval
#restoreH input = 5.513 scaleH refreshnnlist relax eval
#restoreH input = 5.514 scaleH refreshnnlist relax eval
#restoreH input = 5.515 scaleH refreshnnlist relax eval
#restoreH input = 5.516 scaleH refreshnnlist relax eval
#restoreH input = 5.517 scaleH refreshnnlist relax eval
#restoreH input = 5.518 scaleH refreshnnlist relax eval
#restoreH input = 5.519 scaleH refreshnnlist relax eval
#restoreH input = 5.520 scaleH refreshnnlist relax eval
#restoreH input = 5.521 scaleH refreshnnlist relax eval
#restoreH input = 5.522 scaleH refreshnnlist relax eval
#restoreH input = 5.523 scaleH refreshnnlist relax eval
#restoreH input = 5.524 scaleH refreshnnlist relax eval
#restoreH input = 5.525 scaleH refreshnnlist relax eval
#restoreH input = 5.526 scaleH refreshnnlist relax eval
#restoreH input = 5.527 scaleH refreshnnlist relax eval
#restoreH input = 5.528 scaleH refreshnnlist relax eval
#restoreH input = 5.529 scaleH refreshnnlist relax eval
#restoreH input = 5.530 scaleH refreshnnlist relax eval
#restoreH input = 5.531 scaleH refreshnnlist relax eval
#restoreH input = 5.532 scaleH refreshnnlist relax eval
#restoreH input = 5.533 scaleH refreshnnlist relax eval
#restoreH input = 5.534 scaleH refreshnnlist relax eval
#restoreH input = 5.535 scaleH refreshnnlist relax eval
#restoreH input = 5.536 scaleH refreshnnlist relax eval
#restoreH input = 5.537 scaleH refreshnnlist relax eval
#restoreH input = 5.538 scaleH refreshnnlist relax eval
#restoreH input = 5.539 scaleH refreshnnlist relax eval
#restoreH input = 5.540 scaleH refreshnnlist relax eval
#restoreH input = 5.541 scaleH refreshnnlist relax eval
#restoreH input = 5.542 scaleH refreshnnlist relax eval
#restoreH input = 5.543 scaleH refreshnnlist relax eval
#restoreH input = 5.544 scaleH refreshnnlist relax eval
#restoreH input = 5.545 scaleH refreshnnlist relax eval
#restoreH input = 5.546 scaleH refreshnnlist relax eval
#restoreH input = 5.547 scaleH refreshnnlist relax eval
restoreH input = 5.548 scaleH refreshnnlist relax eval
restoreH input = 5.549 scaleH refreshnnlist relax eval
restoreH input = 5.550 scaleH refreshnnlist relax eval
restoreH input = 5.551 scaleH refreshnnlist relax eval
restoreH input = 5.552 scaleH refreshnnlist relax eval
restoreH input = 5.553 scaleH refreshnnlist relax eval
restoreH input = 5.554 scaleH refreshnnlist relax eval
restoreH input = 5.555 scaleH refreshnnlist relax eval
restoreH input = 5.556 scaleH refreshnnlist relax eval
restoreH input = 5.557 scaleH refreshnnlist relax eval
restoreH input = 5.558 scaleH refreshnnlist relax eval
restoreH input = 5.559 scaleH refreshnnlist relax eval
restoreH input = 5.560 scaleH refreshnnlist relax eval
restoreH input = 5.561 scaleH refreshnnlist relax eval
restoreH input = 5.562 scaleH refreshnnlist relax eval
#restoreH input = 5.563 scaleH refreshnnlist relax eval
#restoreH input = 5.564 scaleH refreshnnlist relax eval
#restoreH input = 5.565 scaleH refreshnnlist relax eval
#restoreH input = 5.566 scaleH refreshnnlist relax eval
#restoreH input = 5.567 scaleH refreshnnlist relax eval
#restoreH input = 5.568 scaleH refreshnnlist relax eval
#restoreH input = 5.569 scaleH refreshnnlist relax eval
#restoreH input = 5.570 scaleH refreshnnlist relax eval
#restoreH input = 5.571 scaleH refreshnnlist relax eval
#restoreH input = 5.572 scaleH refreshnnlist relax eval
#restoreH input = 5.573 scaleH refreshnnlist relax eval
#restoreH input = 5.574 scaleH refreshnnlist relax eval
#restoreH input = 5.575 scaleH refreshnnlist relax eval
#restoreH input = 5.576 scaleH refreshnnlist relax eval
#restoreH input = 5.577 scaleH refreshnnlist relax eval
#restoreH input = 5.578 scaleH refreshnnlist relax eval
#restoreH input = 5.579 scaleH refreshnnlist relax eval
#restoreH input = 5.580 scaleH refreshnnlist relax eval
#restoreH input = 5.581 scaleH refreshnnlist relax eval
#restoreH input = 5.582 scaleH refreshnnlist relax eval
#restoreH input = 5.583 scaleH refreshnnlist relax eval
#restoreH input = 5.584 scaleH refreshnnlist relax eval
#restoreH input = 5.585 scaleH refreshnnlist relax eval
#restoreH input = 5.586 scaleH refreshnnlist relax eval
#restoreH input = 5.587 scaleH refreshnnlist relax eval
#restoreH input = 5.588 scaleH refreshnnlist relax eval
#restoreH input = 5.589 scaleH refreshnnlist relax eval
#restoreH input = 5.590 scaleH refreshnnlist relax eval
#restoreH input = 5.591 scaleH refreshnnlist relax eval
#restoreH input = 5.592 scaleH refreshnnlist relax eval
#restoreH input = 5.593 scaleH refreshnnlist relax eval
#restoreH input = 5.594 scaleH refreshnnlist relax eval
#restoreH input = 5.595 scaleH refreshnnlist relax eval
#restoreH input = 5.596 scaleH refreshnnlist relax eval
#restoreH input = 5.597 scaleH refreshnnlist relax eval
#restoreH input = 5.598 scaleH refreshnnlist relax eval
#restoreH input = 5.599 scaleH refreshnnlist relax eval
#restoreH input = 5.600 scaleH refreshnnlist relax eval
#restoreH input = 5.601 scaleH refreshnnlist relax eval
#restoreH input = 5.602 scaleH refreshnnlist relax eval
#restoreH input = 5.603 scaleH refreshnnlist relax eval
#restoreH input = 5.604 scaleH refreshnnlist relax eval
#restoreH input = 5.605 scaleH refreshnnlist relax eval
#restoreH input = 5.606 scaleH refreshnnlist relax eval
#restoreH input = 5.607 scaleH refreshnnlist relax eval
#restoreH input = 5.608 scaleH refreshnnlist relax eval
#restoreH input = 5.609 scaleH refreshnnlist relax eval
#restoreH input = 5.610 scaleH refreshnnlist relax eval
#restoreH input = 5.611 scaleH refreshnnlist relax eval
#restoreH input = 5.612 scaleH refreshnnlist relax eval
#restoreH input = 5.613 scaleH refreshnnlist relax eval
#restoreH input = 5.614 scaleH refreshnnlist relax eval
#restoreH input = 5.615 scaleH refreshnnlist relax eval
#restoreH input = 5.616 scaleH refreshnnlist relax eval
#restoreH input = 5.617 scaleH refreshnnlist relax eval
#restoreH input = 5.618 scaleH refreshnnlist relax eval
#restoreH input = 5.619 scaleH refreshnnlist relax eval
#restoreH input = 5.620 scaleH refreshnnlist relax eval
#restoreH input = 5.621 scaleH refreshnnlist relax eval
#restoreH input = 5.622 scaleH refreshnnlist relax eval
#restoreH input = 5.623 scaleH refreshnnlist relax eval
#restoreH input = 5.624 scaleH refreshnnlist relax eval
#restoreH input = 5.625 scaleH refreshnnlist relax eval
#restoreH input = 5.626 scaleH refreshnnlist relax eval
#restoreH input = 5.627 scaleH refreshnnlist relax eval
#restoreH input = 5.628 scaleH refreshnnlist relax eval
#restoreH input = 5.629 scaleH refreshnnlist relax eval
#restoreH input = 5.630 scaleH refreshnnlist relax eval
#restoreH input = 5.631 scaleH refreshnnlist relax eval
#restoreH input = 5.632 scaleH refreshnnlist relax eval
#restoreH input = 5.633 scaleH refreshnnlist relax eval
#restoreH input = 5.634 scaleH refreshnnlist relax eval
#restoreH input = 5.635 scaleH refreshnnlist relax eval
#restoreH input = 5.636 scaleH refreshnnlist relax eval
#restoreH input = 5.637 scaleH refreshnnlist relax eval
#restoreH input = 5.638 scaleH refreshnnlist relax eval
#restoreH input = 5.639 scaleH refreshnnlist relax eval
#restoreH input = 5.640 scaleH refreshnnlist relax eval
#restoreH input = 5.641 scaleH refreshnnlist relax eval
#restoreH input = 5.642 scaleH refreshnnlist relax eval
#restoreH input = 5.643 scaleH refreshnnlist relax eval
#restoreH input = 5.644 scaleH refreshnnlist relax eval
#restoreH input = 5.645 scaleH refreshnnlist relax eval
#restoreH input = 5.646 scaleH refreshnnlist relax eval
#restoreH input = 5.647 scaleH refreshnnlist relax eval
#restoreH input = 5.648 scaleH refreshnnlist relax eval
#restoreH input = 5.649 scaleH refreshnnlist relax eval
#restoreH input = 5.650 scaleH refreshnnlist relax eval
#restoreH input = 5.651 scaleH refreshnnlist relax eval
#restoreH input = 5.652 scaleH refreshnnlist relax eval
#restoreH input = 5.653 scaleH refreshnnlist relax eval
#restoreH input = 5.654 scaleH refreshnnlist relax eval
#restoreH input = 5.655 scaleH refreshnnlist relax eval
#restoreH input = 5.656 scaleH refreshnnlist relax eval
#restoreH input = 5.657 scaleH refreshnnlist relax eval
#restoreH input = 5.658 scaleH refreshnnlist relax eval
#restoreH input = 5.659 scaleH refreshnnlist relax eval

#
quit
#--------------------------------------------
# Plot Configuration
#
atomradius = [ 0.8 0.5 ] bondradius = 0.3 
win_width = 500 win_height = 500
bondradius = 0.3 bondlength = 2.5 #2.8285 #for Si
atomcolor = orange atomcolor1 = gray90 highlightcolor = purple  bondcolor = green
fixatomcolor = yellow backgroundcolor = gray70
color00 = "orange"  color01 = "purple" color02 = "green"
color03 = "magenta" color04 = "cyan"   color05 = "purple"
color06 = "gray80"  color07 = "white"
#plot_color_windows = [ 2
#                          -10 -3.8 0  #color00 = orange
#                          -3.8 10  1  #color01 = purple
#                     ]
plot_atom_info = 2 #2: real coordinates, 3: energy of atoms
plotfreq = 10
rotateangles = [ 0 0 0 1.2 ]
#openwin alloccolors rotate saverot refreshnnlist plot
#eval sleep quit
#------------------------------------------------------------
#Conjugate-Gradient relaxation
conj_ftol = 1e-6 conj_itmax = 1000 conj_fevalmax = 1000
conj_fixbox = 0 
eval relax eval

quit
