updated charge error and gamess header file syntax

Author: charnley

methods/orbitals/header

@@ -1,4 +1,6 @@
 !   Calculation of molecular orbitals
 !   using a small and quick basis set
- $CONTRL COORD=CART UNITS=ANGS SCFTYP=RHF ICHARG=0 MAXIT=60 $END
+ $CONTRL COORD=CART UNITS=ANGS SCFTYP=RHF
+ icharg=0
+ MAXIT=60 $END
  $BASIS GBASIS=STO NGAUSS=3 $END

methods/orbitals/initialize.php

@@ -89,7 +89,7 @@
         mkdir($calculationType);
 
         shell_exec('babel -xf '.CALPATH.'/'.$calculationType.'/header -ixyz coordinates.xyz -ogamin '.$calculationType.'/'.$hash.'.inp');
-        shell_exec('sed -i "s/ICHARG=0/ICHARG='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
+        shell_exec('sed -i "s/icharg=0/icharg='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
 
         $json['next_step'] = 2;
         $json['next_pct']  = 95;

methods/solvation/header

@@ -1,7 +1,24 @@
 !Calculate solvent effects
- $SYSTEM MWORDS=125 $END
- $BASIS GBASIS=PM3 $END
- $CONTRL SCFTYP=RHF RUNTYP=ENERGY ICHARG=0 $END
- $PCM SOLVNT=WATER MXTS=15000 ICAV=1 IDISP=1 $END
- $TESCAV MTHALL=4 NTSALL=60 $END
- 
+ $system
+    mwords=125
+ $end
+ $basis
+    gbasis=PM3
+ $end
+ $contrl
+    scftyp=RHF
+    runtyp=energy
+    icharg=0
+ $end
+
+ $pcm
+    solvnt=water
+    mxts=15000
+    icav=1
+    idisp=1
+ $end
+ $tescav
+    mthall=4
+    ntsall=60
+ $end
+

methods/solvation/initialize.php

@@ -88,7 +88,7 @@
         mkdir($calculationType);
 
         shell_exec('babel -xf '.CALPATH.'/'.$calculationType.'/header -ixyz coordinates.xyz -ogamin '.$calculationType.'/'.$hash.'.inp');
-        shell_exec('sed -i "s/ICHARG=0/ICHARG='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
+        shell_exec('sed -i "s/icharg=0/icharg='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
 
         $json['next_step'] = 2;
         $json['next_pct']  = 95;

methods/thermodynamic/initialize.php

@@ -89,7 +89,7 @@
         mkdir($calculationType);
 
         shell_exec('babel -xf '.CALPATH.'/'.$calculationType.'/header -ixyz coordinates.xyz -ogamin '.$calculationType.'/'.$hash.'.inp');
-        shell_exec('sed -i "s/ICHARG=0/ICHARG='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
+        shell_exec('sed -i "s/icharg=0/icharg='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
 
         $json['next_step'] = 2;
         $json['next_pct']  = 95;

methods/vibrations/header

@@ -1,5 +1,14 @@
 ! Vibration calculation after a 30 step 
 ! geometry optimisation via PM3
- $BASIS GBASIS=PM3 $END
- $CONTRL SCFTYP=RHF RUNTYP=HESSIAN ICHARG=0 MAXIT=60 $END
+
+ $basis
+  gbasis=PM3
+ $end
+
+ $contrl
+    scftyp=RHF
+    runtyp=hessian
+    icharg=0
+    maxit=60
+ $end
 

methods/vibrations/initialize.php

@@ -89,7 +89,7 @@
         mkdir($calculationType);
 
         shell_exec('babel -xf '.CALPATH.'/'.$calculationType.'/header -ixyz coordinates.xyz -ogamin '.$calculationType.'/'.$hash.'.inp');
-        shell_exec('sed -i "s/ICHARG=0/ICHARG='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
+        shell_exec('sed -i "s/icharg=0/icharg='.$moleculeCharge.'/" '.$calculationType.'/'.$hash.'.inp');
 
         $json['next_step'] = 2;
         $json['next_pct']  = 95;