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
src/Egrad.f90 (revision 11)
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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