#!/bin/sh

# This example demonstrates how one can complete an analytical Hessian calculation
# in three steps without re-doing CPKS for all atoms and the subsequent steps.
# We will define regions for the first and second steps right away. 
# Note that the region for the second step includes atoms of the first one. 
# This is necessary because we want the resulting Hessian in the subsequent steps
# to include the atoms done in the previous calculations.
# First, we calculate the Hessian sub-matrix corresponding to the C atoms.

AMS_JOBNAME=step1 "$AMSBIN/ams" << eor

Task SinglePoint
Properties
    NormalModes Yes
    SelectedRegionForHessian step1
End

System
    Atoms
        C -2.711485799381603 -2.593393872048840 -0.00016442137955 region=step2,step1
        C -1.846368848888818 -1.340467404429865  0.00016453093935 region=step2,step1
        H -2.203636997435432 -3.429266061978078 -0.51549899454129 region=step2
        H -3.673159561801013 -2.414816382275922 -0.51564516686341 region=step2
        H -2.938101685663578 -2.921829124623212  1.03094752484358 region=step2
        H -0.884694282363284 -1.519047266416641  0.51564280107136 
        H -2.354216233206031 -0.504595127574485  0.51550071600252 
        H -1.619753333793463 -1.012031055604717 -1.03094699007257 
    End
    BondOrders
         1 2 1.0
         1 3 1.0
         1 4 1.0
         1 5 1.0
         2 6 1.0
         2 7 1.0
         2 8 1.0
    End
End

Engine ADF
 save TAPE13
EndEngine
eor

# In the second calculation, we add the Hessian sub-matrix corresponding to H atoms 
# of the first methyl group. We use as much data as possible from the first one.
# This includes the part of the analytical Hessian computed for atoms of the "step1" 
# region in the previous calculation.
# We use the adf.rkf file for restart but if the 1st calculation had crashed or 
# stopped uncontrollably, we would have to use the TAPE13 file instead.
#

AMS_JOBNAME=step2 "$AMSBIN/ams" << eor

Task SinglePoint

Properties
    NormalModes Yes
    SelectedRegionForHessian step2
End

LoadSystem
    File step1.results/ams.rkf
End

LoadEngine step1.results/adf.rkf
EngineRestart step1.results/adf.rkf
eor

# In the third calculation, we do not use the SelectedRegionForHessian key, because
# we want the full Hessian. In this calculation we use data from the second step.

AMS_JOBNAME=step3 "$AMSBIN/ams" << eor

Task SinglePoint

Properties
    NormalModes Yes
End

LoadSystem
    File step2.results/ams.rkf
End

LoadEngine step2.results/adf.rkf
EngineRestart step2.results/adf.rkf
eor