## Revision 11

examples/Test/Dep_tscan_movie (revision 11)
51 51
 unset key

52 52
 set term $DefTerm  53 53 EOF  54 let ItM=ItMax-1  54 let ItM=ItMax-2  55 55 for i in seq 0$ItM

56 56
  do

57 57
 xyz2scan ${Nom}${ExtF}.${i} > /dev/null  58 58  mv Scan.dat${Nom}_${i}.dat  59  echo "plot \"HCN_irc.dat\" u 1:3 w l lw 2" >>${NGplot}

59
 echo "plot \"HCN_irc.dat\" u 1:3 w l ls 1" >> ${NGplot}  60 60  if [ "$PES" != "" ]; then

61
  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l 2" >> ${NGplot}  61  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l ls 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l ls 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l ls 2" >>${NGplot}

62 62
 fi

63 63
 if [ -s ${Nom}_spline.${i} ]; then

64
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 1" >> ${NGplot}  65  echo "replot \"${Nom}_spline.${i}\" u 2:4 w l ls 1" >>${NGplot}

64
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 5" >> ${NGplot}  65  echo "replot \"${Nom}_spline.${i}\" u 2:4 w l ls 5" >>${NGplot}

66 66
 elif [  -s ${Nom}_dbgtgt_${i}.dat ]; then

67
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 1" >> ${NGplot}  68  echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l ls 1" >> ${NGplot}  67  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>${NGplot}

68
 echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l ls 4" >>${NGplot}

69 69
 else

70
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 1" >> ${NGplot}  70  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>${NGplot}

71 71
fi

72 72
 if [ "$Tgt" != "" ]; then  73  echo "replot \"${Nom}_tgt_${i}.dat\" u 1:3 w l" >>${NGplot}

73
  echo "replot \"${Nom}_tgt_${i}.dat\" u 1:3 w l ls 4" >> ${NGplot}  74 74  fi  75 75  IMov=echo$i | awk '{ It="000" $1; l=length(It); print substr(It,l-2,3)}'   76 76  cat <<EOF >>${NGplot}

......
82 82
 set term $DefTerm  83 83 EOF  84 84  done  85 let i=ItMax  85 let i=ItMax-1  86 86  awk -f$WDir/Path2dat.awk  ${Nom}.${i} > ${Nom}_${i}.dat

87
 echo "plot \"HCN_irc.dat\" u 1:3 w l lw 2" >> ${NGplot}  87  echo "plot \"HCN_irc.dat\" u 1:3 w l ls 1" >>${NGplot}

88 88
 if [ "$PES" != "" ]; then  89  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l 2" >>${NGplot}

89
  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l ls 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l ls 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l ls 2" >> ${NGplot}  90 90  fi  91 91  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 1" >>${NGplot}

92 92
 IMov=echo $i | awk '{ It="000"$1; l=length(It); print substr(It,l-2,3)}' 

examples/Test/Dep_tscan_p (revision 11)
58 58
 clear

59 59
 set xrange [1.:2.5]

60 60
 set yrange [-10:190]

61
 plot "HCN_irc.dat" u 1:3 w l

61
 plot "HCN_irc.dat" u 1:3 t "IRC" w l ls 1

62 62
EOF

63 63
 if [ "$PES" != "" ]; then  64  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l 2" >>$NomGplot

64
  echo "replot \"HCN_PES_2D.dat\" u 1:2 t \"\" w l ls 2, \"HCN_PES_2D.dat\" u 1:(-\$2) t \"\" w l ls 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) t \"\" w l ls 2" >> $NomGplot  65 65  fi  66 66  if [ "$Ext" = "_cart" ]; then

67 67
   if [ -s ${Nom}_spline.${i} ]; then

68
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >> $NomGplot  69  echo "replot \"${Nom}_spline.${i}\" u 2:4 w l" >>$NomGplot

68
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w p  ls 5" >> $NomGplot  69  echo "replot \"${Nom}_spline.${i}\" u 2:4 t \"Spline\" w l ls 5" >>$NomGplot

70 70
   elif [  -s ${Nom}_dbgtgt.${i} ]; then

71
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >> $NomGplot  72  echo "replot \"${Nom}_dbgtgt.${i}\" u 2:(\$4*180./pi) w l" >> $NomGplot  71  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>$NomGplot

72
     echo "replot \"${Nom}_dbgtgt.${i}\" u 2:(\$4*180./pi) t \"Tangents\" w l ls 4" >>$NomGplot

73 73
   else

74
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp 5" >> $NomGplot  74  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>$NomGplot

75 75
   fi

76 76
 else

77 77
   if [ -s ${Nom}_spline_${i}.dat ]; then

78
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >> $NomGplot  79  echo "replot \"${Nom}_spline_${i}.dat\" u 1:3 w lp" >>$NomGplot

78
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 5" >> $NomGplot  79  echo "replot \"${Nom}_spline_${i}.dat\" u 1:3 w lp ls 5" >>$NomGplot

80 80
   elif [  -s ${Nom}_dbgtgt_${i}.dat ]; then

81
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >> $NomGplot  82  echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 1:3 w l" >>$NomGplot

81
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >> $NomGplot  82  echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 1:3 w l ls 4" >>$NomGplot

83 83
   else

84
     echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp 5" >> $NomGplot  84  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>$NomGplot

85 85
   fi

86 86
 fi

87 87
 if [ "$Tgt" != "" ]; then  88  echo "replot \"${Nom}_tgt_${i}.dat\" u 1:3 w l" >>$NomGplot

88
  echo "replot \"${Nom}_tgt_${i}.dat\" u 1:3 w l ls 1" >> $NomGplot  89 89  fi  90 90  echo "pause -1" >>$NomGplot

91 91
 done

92
let i=ItMax

92
 let i=ItMax

93 93
 xyz2scan ${Nom}${Ext}.${i} > /dev/null  94 94  mv Scan.dat${Nom}_${i}.dat  95 95  cat <<EOF >>$NomGplot

96 96
 clear

97 97
 set xrange [1.:2.5]

98 98
 set yrange [-10:190]

99
 plot "HCN_irc.dat" u 1:3 w l

99
 plot "HCN_irc.dat" u 1:3 t " IRC" w l ls 1

100 100
EOF

101 101
 if [ "$PES" != "" ]; then  102  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l 2" >>$NomGplot

102
  echo "replot \"HCN_PES_2D.dat\" u 1:2  t \"\" w l ls 2, \"HCN_PES_2D.dat\" u 1:(-\$2) t \"\" w l ls 2,\"HCN_PES_2D.dat\" u 1:(360-\$2)  t \"\" w l ls 2" >> $NomGplot  103 103  fi  104 104  if [ -s${Nom}_spline.${i} ]; then  105  echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >>$NomGplot

106
 echo "replot \"${Nom}_spline.${i}\" u 2:4 w l" >> $NomGplot  105  echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 5" >>$NomGplot

106
 echo "replot \"${Nom}_spline.${i}\" u 2:4 w l ls 5" >> $NomGplot  107 107  elif [ -s${Nom}_dbgtgt_${i}.dat ]; then  108  echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >>$NomGplot

109
 echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l" >>$NomGplot

108
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >> $NomGplot  109  echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l ls 4" >> $NomGplot  110 110  else  111  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp 5" >>$NomGplot

111
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >> $NomGplot  112 112 fi  113 113  echo "pause -1" >>$NomGplot

114 114
chmod u+x $NomGplot  examples/Test/Dep_tscan_m (revision 11) 1 1 #!/bin/bash  2 2 export LANG=C  3 if [$# -lt 3 ]; then

3
if [ $# -lt 1 ]; then  4 4  echo "Use:$0 File.out [PES] [T]"

5 5
 exit

6 6
fi

......
25 25
 set pointsize 2

26 26
 unset key

27 27
EOF

28
let ItM=ItMax-1

28
let ItM=ItMax-2

29 29
for i in seq 0 $ItM  30 30  do  31 31  xyz2scan${Nom}_cart.${i} > /dev/null  ...... 33 33  cat <<EOF >>$NomGplot

34 34
 set multiplot

35 35
 set origin 0.,0.

36
 set size 0.5

36
 set size 0.5,1.

37 37
 clear

38 38
 set xrange [1.:2.5]

39 39
 set yrange [-10:190]

40
 plot "HCN_irc.dat" u 1:3 w l

40
 plot "HCN_irc.dat" u 1:3 w l ls 1

41 41
EOF

42 42
 if [ "$PES" != "" ]; then  43  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l 2" >>$NomGplot

43
  echo "replot \"HCN_PES_2D.dat\" u 1:2 t \"\" w l ls 2, \"HCN_PES_2D.dat\" u 1:(-\$2) t \"\" w l ls 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) t \"\"  w l ls 2" >> $NomGplot  44 44  fi  45 45  if [ -s${Nom}_spline.${i} ]; then  46  echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >>$NomGplot

47
 echo "replot \"${Nom}_spline.${i}\" u 2:4 w l" >> $NomGplot  46  echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 5" >>$NomGplot

47
 echo "replot \"${Nom}_spline.${i}\" u 2:4 w l ls 5" >> $NomGplot  48 48  elif [ -s${Nom}_dbgtgt_${i}.dat ]; then  49  echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >>$NomGplot

50
 echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l" >>$NomGplot

49
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp 5" >> $NomGplot  50  echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l ls 4" >> $NomGplot  51 51  else  52  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp 5" >>$NomGplot

52
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >> $NomGplot  53 53 fi  54 54  if [ "$Tgt" != "" ]; then

55
  echo "replot \"${Nom}_tgt_${i}.dat\" u 1:3 w l" >> $NomGplot  55  echo "replot \"${Nom}_tgt_${i}.dat\" u 1:3 w l ls 4" >>$NomGplot

56 56
 fi

57 57
 cat <<EOF >>  $NomGplot  58 58  set origin .505,0.  59 # set size 0.5  59 # set size 0.5,1.  60 60  clear  61 61  set yrange$yr

62 62
 set xrange [-10:190]

63 63
EOF

64
 echo "plot \"${Nom}_${i}.dat\" u 3:4 t \"E\" w lp" >> $NomGplot  64  echo "plot \"${Nom}_${i}.dat\" u 3:4 t \"E\" w lp ls 1" >>$NomGplot

65 65
 echo "unset multiplot" >> $NomGplot  66 66  echo "pause -1" >>$NomGplot

67 67
 done

68
let i=ItMax

68
let i=ItMax-1

69 69
 xyz2scan ${Nom}_cart.${i} > /dev/null

70 70
 mv Scan.dat ${Nom}_${i}.dat

71 71
 cat <<EOF >>  $NomGplot  72 72  set multiplot  73 73  set origin 0.,0.  74 # set size 0.5  74 # set size 0.5,1.  75 75  clear  76 76  set xrange [1.:2.5]  77 77  set yrange [-10:190]  78  plot "HCN_irc.dat" u 1:3 w l  78  plot "HCN_irc.dat" u 1:3 t "IRC" w l ls 1  79 79 EOF  80 80  if [ "$PES" != "" ]; then

81
  echo "replot \"HCN_PES_2D.dat\" u 1:2 w l 2, \"HCN_PES_2D.dat\" u 1:(-\$2) w l 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) w l 2" >> $NomGplot  81  echo "replot \"HCN_PES_2D.dat\" u 1:2 t \"\" w l ls 2, \"HCN_PES_2D.dat\" u 1:(-\$2) t \"\" w l ls 2,\"HCN_PES_2D.dat\" u 1:(360-\$2) t \"\" w l ls 2" >>$NomGplot

82 82
 fi

83 83
 if [ -s ${Nom}_spline.${i} ]; then

84
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >> $NomGplot  85  echo "replot \"${Nom}_spline.${i}\" u 2:4 w l" >>$NomGplot

84
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w p ls 5" >> $NomGplot  85  echo "replot \"${Nom}_spline.${i}\" u 2:4 w l ls 5" >>$NomGplot

86 86
 elif [  -s ${Nom}_dbgtgt_${i}.dat ]; then

87
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w p 5" >> $NomGplot  88  echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l" >> $NomGplot  87  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>$NomGplot

88
 echo "replot \"${Nom}_dbgtgt_${i}.dat\" u 2:(\$4*180./pi) w l ls 4" >>$NomGplot

89 89
 else

90
 echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp 5" >> $NomGplot  90  echo "replot \"${Nom}_${i}.dat\" u 1:3 w lp ls 5" >>$NomGplot

91 91
fi

92 92
 cat <<EOF >>  $NomGplot  93 93  set origin .505,0.  94 # set size 0.5  94 # set size 0.5,1.  95 95  clear  96 96  set yrange$yr

97 97
 set xrange [-10:190]

98 98
EOF

99
 echo "plot \"${Nom}_${i}.dat\" u 3:4 t \"E\" w lp" >> $NomGplot  99  echo "plot \"${Nom}_${i}.dat\" u 3:4 t \"E\" w lp ls 1" >>$NomGplot

100 100
 echo "unset multiplot" >> $NomGplot  101 101  echo "pause -1" >>$NomGplot

102 102

103 103
chmod u+x ./$NomGplot  104 echo "./$NomGplot      to see the path"

104
echo "./\$NomGplot      to see the path"

src/CalcRmsd.f90 (revision 11)
56 56
      real(KREAL) ::  U(3,3), rmsd

57 57
      LOGICAL  FRot,FAlign,Debug

58 58

59
      REAL(KREAL) :: Coord1(3,Nat), Coord2(3,Nat)

59
      REAL(KREAL),ALLOCATABLE :: Coord1(:,:), Coord2(:,:) ! 3,Nat

60 60
      real(KREAL) ::  x0c1,y0c1,z0c1, xc2,yc2,zc2

61 61


62 62

......
76 76

77 77
      debug=valid('CalcRmsd').OR.valid('align').OR.valid('alignpartial')

78 78

79
      if (debug) Call Header("Entering CalcRmsd")

80

81
      if (debug) THEN

82
         WRITE(*,*) "NAt=",NAt

83
         WRITE(*,*) x0

84
         WRITE(*,*) y0

85
         WRITE(*,*) z0

86
      END IF

87

88
      ALLOCATE(Coord1(3,Nat),Coord2(3,Nat))

79 89
  ! calculate the barycenters, centroidal coordinates, and the norms

80 90
      x_norm = 0.0d0

81 91
      y_norm = 0.0d0

......
86 96
      yc2=0.

87 97
      zc2=0.

88 98
      do ia=1,Nat

99
         if (debug) WRITE(*,'(A,I5,4(1X,F10.4))') 'ia...',ia,x0(ia), &

100
                             x2(ia),x0c1,xc2

89 101
         x0c1=x0c1+x0(ia)

90 102
         xc2=xc2+x2(ia)

91 103
         y0c1=y0c1+y0(ia)

92 104
         yc2=yc2+y2(ia)

93 105
         z0c1=z0c1+z0(ia)

94 106
         zc2=zc2+z2(ia)

95
!         if (debug) WRITE(*,'(A,I5,4(1X,F10.4))') 'ia...',ia,x0(ia),

96
!     &                        x2(ia),x0c1,xc2

107
         if (debug) WRITE(*,'(A,I5,4(1X,F10.4))') 'ia...',ia,x0(ia), &

108
                             x2(ia),x0c1,xc2

97 109
      END DO

98 110
      x0c1=x0c1/dble(Nat)

99 111
      y0c1=y0c1/dble(Nat)

......
195 207
         END DO

196 208
      END IF

197 209

198
      END

210
      DEALLOCATE(Coord1,Coord2)

211

212
    END subroutine CalcRmsd

121 121
           Z(1:Nat)=GeomCart(1:Nat,3)

122 122
        END IF

123 123

124
        if (debug) then

124 125
           WRITE(*,*) "Geom before orientation after reorderring"

125 126
           WRITE(*,*) Nat

126 127
           WRITE(*,*) ""

......
157 158
              GeomCart(Iat,3)=Z(I)

158 159
           END DO

159 160
        END IF

161
     END IF

162

160 163
  CASE ('BAKER')

161 164
     XPrimRef=XPrimitiveF(IGeom,:)

162 165
     IF (Flag_Opt_Geom) THEN


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