package SCIGRESS;
use Exporter;
@ISA = qw(Exporter);

#公開したいサブルーチン
@EXPORT = qw();

#use lib "d:/Programs/Perl/lib";

use strict;
use File::Basename;

use ProgVars;
use Utils;
use GraphData;
use Sci::Science;
use Sci::EnergyBandArray;
#use MyTk::GraphFrameArray;

use Crystal::Crystal;
use Crystal::AtomType;
use Crystal::AtomSite;
use Crystal::XCrySDen;
use Crystal::CIF;

#===============================================
# スクリプト大域変数
#===============================================
my $LF = "<br>\n";
my $DirectorySeparator = Deps::DirectorySeparator(); #"\\";

#===============================================
# パス（読み込みDB）
# Web関係変数
# CGI の仮想パス
# プログラム名
#===============================================
my $Program        = ProgVars::Program();
my $ProgramDir     = ProgVars::ProgramDir();
my $ProgramOldDir  = ProgVars::ProgramOldDir();
my $SCIGRESSDir    = ProgVars::SCIGRESSDir();
my $WebRootDir     = ProgVars::WebRootDir();
my $KListDBDir     = ProgVars::KListDBDir();

#============================================================
#　変数等取得、再定義関数
#============================================================
sub ClearAll      { my $this=shift; delete $this->{FileType}; delete $this->{DataArray}; }
sub FileType      { return shift->{FileType}; }
sub FileName      { return shift->{FileName}; }
sub SetFileName   { my ($this,$f)=@_; return $this->{'FileName'} = $f; }
sub SetSampleName { my ($this,$n)=@_; return $this->{'SampleName'} = $n; }
sub SampleName    { return shift->{'SampleName'}; }

#============================================================
#　継承クラスで定義しなおす関数
#============================================================
sub CheckFileType
{
	my ($path) = @_;
	my ($drive, $dir, $filename, $ext, $lastdir, $filebody) = Deps::SplitFilePath($path);
	if($filename =~ /\.sim$/i) {
		return "SCIGRESS sim file";
	}
	elsif($filename =~ /\.txt$/i) {
		return "SCIGRESS sim-converted text file";
	}
	elsif($filename =~ /\.lst$/i) {
		return "SCIGRESS output LST file";
	}
	return undef;
}

#============================================================
#　コンストラクタ、デストラクタ
#============================================================
sub new
{
	my ($module) = @_;
	my $this = {};
	bless $this;
	return $this;
}

sub DESTROY { my $this = shift; }

#============================================================
#　一般関数
#============================================================
sub SaveBDLFile
{
	my ($this, $Crystal, $SaveFile, $ChooseRandomly, $IsPrint) = @_;
	$ChooseRandomly = 0 if(!defined $ChooseRandomly);
	$IsPrint        = 1 if(!defined $IsPrint);

	my $out = JFile->new($SaveFile, "w");
	unless($out) {
print("<br><br>Error: Can not write to [$SaveFile]<br><br>\n") if($IsPrint);
		return;
	}

	my $CrystalName = $Crystal->CrystalName();
	my $SuperLattice = $Crystal->GetCSuperLattice();
	$Crystal = $SuperLattice if($SuperLattice);

	my ($a, $b, $c, $alpha, $beta, $gamma) = $Crystal->LatticeParameters();
	my @AtomTypeList = $Crystal->GetCAtomTypeList();
	my $nAtomType = @AtomTypeList;
	my @AtomSiteList = $Crystal->GetCExpandedAtomSiteList();
	my $nAtomSite = @AtomSiteList;
	my %nAtom;
	for(my $i = 0 ; $i < $nAtomSite ; $i++) {
		my $site     = $AtomSiteList[$i];
		my $atomname = $site->AtomNameOnly();
		$nAtom{$atomname}++;
	}
print "nType: $nAtomType  nSite: $nAtomSite\n" if($IsPrint);

	my $line = 1;
if($IsPrint) {
	printf("Latt: %8f  %8f  %8f<br>\n", $a, $b, $c);
	printf("Latt: %8f  %8f  %8f<br>\n", $alpha, $beta, $gamma);
	printf("nAtomType: %2d  %2d<br>\n", $nAtomType, 2);
}
	$out->printf("%06d   %8f  %8f  %8f\n", $line++, $a, $b, $c);
	$out->printf("%06d   %8f  %8f  %8f\n", $line++, $alpha, $beta, $gamma);
	$out->printf("%06d   %2d  %2d\n", $line++, $nAtomType, 2);
	for(my $ia = 0 ; $ia < $nAtomType ; $ia++) {
		my $type     = $AtomTypeList[$ia];
		my $atomname = $type->AtomNameOnly();
		my $charge   = $type->Charge();
		my $mass     = $type->AtomicMass();
if($IsPrint) {
	printf("%-2s %3d  %3d  %3d<br>\n", $atomname, 1, $nAtom{$atomname}, 0);
}
		$out->printf("%06d   %-6s                           %3d  %3d  %3d\n", $line++, $atomname, 1, $nAtom{$atomname}, 0);
		for(my $is = 0 ; $is < $nAtomSite ; $is++) {
			my $site      = $AtomSiteList[$is];
			my $atomname1 = $site->AtomNameOnly();
			my ($x,$y,$z) = $site->Position(1);
			next if($atomname1 ne $atomname);
if($IsPrint) {
	printf("%-2s %8.3f %8.6f %8.6f %8.6f %8.4f<br>\n", $atomname, $charge, $x, $y, $z, $mass);
}
			$out->printf("%06d   %-4s %8.3f %15f %15f %15f %8.5f\n", $line++, $atomname, $charge, $x, $y, $z, $mass);
		}
	}
	$out->Close();
}

sub ReadHeadingInforFromTXTFile
{
	my ($this, $in) = @_;

	my ($nMDStep, $iOutputStep0, $nOutputInterval, @AtomTypes, $NATOM, $KMOL, @NUMMOL, @NUMATOM);
	my $line = $in->SkipTo("1st Record");
	return undef if(!defined $line);

	$line = $in->SkipTo("NSTEP");
	($nMDStep) = ($line =~ /=\s*(\d+)/);
print "nMDStep: $nMDStep\n";
	$line = $in->SkipTo("MINIT");
	($iOutputStep0) = ($line =~ /=\s*(\d+)/);
print "iOutputStep0: $iOutputStep0\n";
	$line = $in->SkipTo("MINTV");
	($nOutputInterval) = ($line =~ /=\s*(\d+)/);
print "nOutputInterval: $nOutputInterval\n";

	$line = $in->SkipTo("NATOM");
	($NATOM) = ($line =~ /=\s*(\d+)/);
print "nAtom: $NATOM\n";
	$line = $in->SkipTo("KMOL");
	($KMOL) = ($line =~ /=\s*(\d+)/);
print "KMOL: $KMOL\n";

	$line = $in->SkipTo("I\\s+CHAMOL");
	for(my $i = 0 ; $i < $KMOL ; $i++) {
		$line = $in->ReadLine();
		my ($ID, $name, $IDYNAM, $NUMMOL, $NUMATOM, $nBond, $KINDAT) = Utils::Split("\\s+", $line);
		$name =~ s/\d//g;
		$AtomTypes[$i] = $name;
		$NUMMOL[$i]  = $NUMMOL;
		$NUMATOM[$i] = $NUMATOM;
print "at[$i]: $AtomTypes[$i] [NUMOL=$NUMMOL][NUMATOM=$NUMATOM]\n";
	}

	return ($nMDStep, $iOutputStep0, $nOutputInterval, $NATOM, $KMOL, \@AtomTypes, \@NUMMOL, \@NUMATOM);
}

sub ReadNextStructureFromTXTFile
{
	my ($this, $nStep, $in, $SampleName, $NATOM, $KMOL, $pAtomTypes, $pNUMMOL, $pNUMATOM) = @_;

	my $Crystal = new Crystal;
	$Crystal->SetCrystalName($SampleName);
	$Crystal->SetSampleName($SampleName);
	for(my $i = 0 ; $i < $NATOM ; $i++) {
		$Crystal->AddAtomType($pAtomTypes->[$i], 0);
	}

	my $line = $in->SkipTo("#\\s+STEP\\s+=");
	return undef if(!defined $line);

	$line = $in->SkipTo("Lattice Constants");
	$in->ReadLine();
	$line = $in->ReadLine();
	my ($a, $b, $c) = Utils::Split("\\s+", $line);
	$in->ReadLine();
	$line = $in->ReadLine();
	my ($alpha, $beta, $gamma) = Utils::Split("\\s+", $line);
	$a += 0;
	$b += 0;
	$c += 0;
	$alpha += 0;
	$beta  += 0;
	$gamma += 0;
	$Crystal->SetLatticeParameters($a, $b, $c, $alpha, $beta, $gamma);
print "latt: $a, $b, $c,   $alpha, $beta, $gamma\n";

	$in->SkipTo("Lattice Coordinate");
	$in->ReadLine();
	$in->ReadLine();
	$in->ReadLine();
	$in->ReadLine();
	for(my $i = 0 ; $i < $KMOL ; $i++) {
		my $atomtype = $pAtomTypes->[$i];
		my $i1 = $i + 1;
		for(my $im = 0 ; $im < $pNUMMOL->[$i] ; $im++) {
			for(my $ia = 0 ; $ia < $pNUMATOM->[$i] ; $ia++) {
				$line = $in->ReadLine();
				my ($I, $J, $K, $x, $y, $z) = Utils::Split("\\s+", $line);
#print "at: $atomtype\n";
				$Crystal->AddAtomSite("$atomtype$i1", $atomtype, $x, $y, $z, 1.0);
#if($nStep % 50 == 0) {
#	print("$nStep:$i:$im:$ia: [$atomtype] ($x, $y, $z)\n");
#}
			}
		}
	}
	$Crystal->ExpandCoordinates();

	return $Crystal;
}

sub ReadAtomTypesFromCSFFile
{
	my ($this, $LSTPath) = @_;

	my %NameHash;
	my @AtomTypes;
	my $nAtomTypes = 0;

	my $in = new JFile($LSTPath, "rb");
	return () if(!$in);

	$in->SkipTo("ID\\s+PDBName\\s+GroupType");
	while(1) {
		my $line = $in->ReadLine();
		my ($ID, $PDBName, $GroupType, $SSpdb, $AAcode, $name, $Chain) = Utils::Split("\\s+", $line);
		last if($ID !~ /^\d+$/);

		$name =~ s/\d//g;
		if(defined $NameHash{$name}) {
		}
		else {
			$NameHash{$name}++;
			$AtomTypes[$nAtomTypes] = $name;
			$nAtomTypes++;
		}
	}
#for(my $i = 0 ; $i < $nAtomTypes ; $i++) {
#	print "name[$i]: $AtomTypes[$i]\n";
#}

	$in->Close();
	return @AtomTypes;
}

sub ReadAtomTypesFromLSTFile
{
	my ($this, $LSTPath) = @_;

	my ($nAtom, $KMOL, $nKAtom);
	my @AtomTypes;

	my $in = new JFile($LSTPath, "rb");
#binmode(STDOUT);
	return () if(!$in);

	$in->SkipTo("----\\s+NATOM");
	my $line = $in->ReadLine();
	($nAtom, $KMOL, $nKAtom) = Utils::Split("\\s+", $line);
print "n: $nAtom, $KMOL, $nKAtom\n";
	for(my $i = 0 ; $i < $nKAtom ; $i++) {
		$in->SkipTo("----\\s+CHAMOL");
		$line = $in->ReadLine();
#print "l: $line\n";
#		$AtomTypes[$i] = $line;
#print "l: [$AtomTypes[$i]]\n";
#		$AtomTypes[$i] =~ s/\s.*$//;
		($AtomTypes[$i]) =~ /(\w+)\x00/;
print "$i: [$AtomTypes[$i]]\n";
	}

	$in->Close();
	return @AtomTypes;
}

1;