mini

mini mini petite souris



This C-program optimises (minimum or TS) variables (can be a geometry or something else) by calling a "script" (you have to make it! So it can be linked to any program!).
It can also calculate gradient, hessian matrix, frequencies.

In the commands the upper or lower case doesn't matter. However, it can be important in the variable names.

It has a restart capability.

All commands finish by an 'end'.

You have to separate words (numbers) by at least one blank space.

list of commands.

some examples.

download a copy of mini mini.tar.gz
uncompress and compile it. 


gunzip mini.tar.gz
tar xvf mini.tar
cd mini
make

There are more examples in mini/examples

a small example: optimisation of water with molpro. 

data
  R = 2. bohr 1
  A = 109. degree -1
end

The program minimises R (1) end maximises A (-1). You should get the linear transition state.

However, you need a script to link mini to molpro (const, the script name by default).
It must be executable. So you should use this command 'chmod u+x const' in unix. 


#!/bin/ksh

echo "***,HOH sto-3g RHF
">x.inpm
cat geom>>x.inpm
echo "zmat,noorient
O1
H2,O1,R
H3,O1,R,H2,A
endz
basis=sto-3g
 int
 hf
 ">>x.inpm

 molpro.run x
grep "SCF STATE 1.1 ENERGY" x.outm|awk '{print $5}'>energ
grep "NO CONVERGE" x.outm|awk '{print 0}'>>energ
echo 1 >> energ

The variables are put in the file 'geom', and the program reads the energy in the file 'energ'.

The first part of the scrip generates an input file for molpro (until the last >> x.inpm). It's mostly the input file of molpro.

molpro.run x : execution of molpro.

extraction of the energy of the output file (x.outm, here) and add a flag (0 or 1) for the convergence.

you get: 


data

 R = 2.000000000000 bohr 1
 A = 109.000000000000 degree -1




opt = 1
hess = 0
grad = 0
ene = 2
 R = 1.762380589233 bohr 1
 A = 179.999982248148 degree -1

 energie = -74.852480660000

List of commands:

examples:

  1. example: optimisation and frequencies of Cl-O
  2. example: optimisation and frequencies of H2O
  3. example: optimisation and hessian of H2O

  1. data: optimisation and frequencies of Cl-O 
    fichiers
  const = const_AB
end
controle
  test_opt = 1
  test_ene = 0
  test_grad = 0
  test_hess = 2
  test_freq = 1
end
data
x1 =  0.000000000 bohr 0
y1 =  0.000000000 bohr 0
z1 =  0.000000000 bohr 0
x2 =  0.000000000 bohr 0
y2 =  0.000000000 bohr 0
z2 =  2.970000000 bohr 1
end
param
  deriv = 0.005
  conv_energie = 5.e-6
  conv_deplace = 5.e-5
  max_deplace =  0.1
end
masses
15.994915
34.968853
end
    script: const_AB 
    #!/bin/ksh

awk '{t[NR]=$3}
END {
#
Req=2.9725
k=0.305573
#
#for (i=1;i<7;i++) print t[i]
 x=t[1]-t[4]
 y=t[2]-t[5]
 z=t[3]-t[6]
 r=sqrt(x*x+y*y+z*z)
 print 0.5*k*(r-Req)*(r-Req)
}' geom >energ

echo 1 >>energ

  2. data: optimisation and frequencies of H2O 
    fichiers
  const = const_h2o_cart
end
controle
  test_opt = 1
  test_ene = 0
  test_grad = 0
  test_hess = 2
  test_freq = 1
end
cart
    na = 3
    prog = gamess
    bohr = t
    convert = f
    opt =
          0 0 0
          1 0 1
          1 0 1
end
 O           8.0     0.0000000000        0.0000000000       -0.1344680200
 H           1.0     1.4326043750        0.0000000000        1.0670525220
 H           1.0    -1.4326043750        0.0000000000        1.0670525220
param
  deriv = 0.01
  conv_energie = 1.e-4
  conv_deplace = 1.e-3
  max_deplace =  0.1
end
    script: const_h2o_cart

    you can use one of these 2 scripts:
    - the first one use nawk unix command (or gawk). I you don't have it, use the second one.
    - the second use another program: cart.

    The hessian matrix (3*3) has been calculated in example 3.

    first script

    #!/bin/ksh


nawk '{t[NR]=$3}
END {

# vector 1 (OH_1)
vx1=t[1]-t[4]
vy1=t[2]-t[5]
vz1=t[3]-t[6]
d1=sqrt(vx1*vx1+vy1*vy1+vz1*vz1)

# vector 1 (OH_2)
vx2=t[1]-t[7]
vy2=t[2]-t[8]
vz2=t[3]-t[9]
d2=sqrt(vx2*vx2+vy2*vy2+vz2*vz2)

#angle HOH
c=(vx1*vx2+vy1*vy2+vz1*vz2)/(d1*d2)
s=sqrt(1.0-c*c)
angle=atan2(s,c)

#print d1" "d2" "angle

#hessian3*3
h11=0.65407272
h22=0.65407580
h33=0.29688606

h12=-0.03064230
h13=0.03770003
h23=0.03769997

#energy (harmonic)
r0=1.8697612
a0=1.7458023

r1=d1-r0
r2=d2-r0
a1=angle-a0

e = 0.5*( r1*r1*h11 + r2*r2*h22 + a1*a1*h33)
e = e + ( r1*r2*h12 + r1*a1*h13 + r2*a1*h23)
print e
}' geom >energ

echo 1 >> energ

    second script

    #!/bin/ksh

echo " \$lect na=3 prog='g92' convert=.false. \$end" >dat

awk '{t[NR]=$3}
END {
print " 1 8 "t[1]" "t[2]" "t[3]
print " 2 1 "t[4]" "t[5]" "t[6]
print " 2 1 "t[7]" "t[8]" "t[9]}' geom >>dat


echo " \$oper \$end

 \$zmat nb=3 \$end
1
2 1
3 1 2
 \$fiop
 \$fini" >> dat

cart geom1


awk '{t[NR]=$2}
END {

h11=0.65407272
h22=0.65407580
h33=0.29688606

h12=-0.03064230
h13=0.03770003
h23=0.03769997

r0=1.8697612
a0=1.7458023

r1=t[1]-r0
r2=t[2]-r0
a1=t[3]*0.0174553292-a0

e = 0.5*( r1*r1*h11 + r2*r2*h22 + a1*a1*h33)
e = e + ( r1*r2*h12 + r1*a1*h13 + r2*a1*h23)
print e
}' geom1 >energ

echo 1 >> energ

  3. data: optimisation of H2O and hessian matrix. 
    fichiers
 const = const_h2o_h33
end
controle
  test_opt = 0
  i_ts_min = 0
  test_hess = 2
  test_freq = 0
end
data
  R1 = 2. bohr 1
  R2 = 2. bohr 1
  A  = 109. degree 1
end
param
  deriv = 0.01
  conv_energie = 1.e-6
  conv_deplace = 1.e-4
  max_deplace =  0.1
end
    script: const_h2o_h33 
    echo "***,HOH sto-3g RHF
memory,0.5,m
">x.inpm
cat geom>>x.inpm
echo "zmat,nosym,noorient
O1
H2,O1,R1
H3,O1,R2,H2,A
endz
basis=sto-3g
 int
 hf

show[1,f25.15],energy

 ">>x.inpm

 molpro.run x
grep "ENERGY / AU" x.outm|awk '{print $5}'>energ
grep "NO CONVERGE" x.outm|awk '{print 0}'>>energ
echo 1 >> energ

Background: Ptiluc ici (in French)