pulling useful information from G03/G09 calculations

A short while after I began grad school, which was years ago now, I realized that checking on the progress of a G03/G09 calculation often required sifting through massive amounts of detritus. Rather than use less and then search through the entire file, I began learning grep, sed, and awk. This post deals with the first command, grep, and how to make custom versions that can pull out specific information. Perhaps the example I use most often is checking on the progress of a geometry optimization. G03/G09 spit out the 4 convergence criteria after each iteration, as shown below.

$ grep -iA3 "maximum force" test.log
 Maximum Force            0.009759     0.000450     NO 
 RMS     Force            0.001640     0.000300     NO 
 Maximum Displacement     0.380695     0.001800     NO 
 RMS     Displacement     0.042164     0.001200     NO 
--
 Maximum Force            0.001122     0.000450     NO 
 RMS     Force            0.000200     0.000300     YES
 Maximum Displacement     0.117795     0.001800     NO 
 RMS     Displacement     0.034630     0.001200     NO 
--
 Maximum Force            0.000796     0.000450     NO 
 RMS     Force            0.000091     0.000300     YES
 Maximum Displacement     0.290041     0.001800     NO 
 RMS     Displacement     0.065495     0.001200     NO 
--
 Maximum Force            0.000462     0.000450     NO 
 RMS     Force            0.000095     0.000300     YES
 Maximum Displacement     0.245764     0.001800     NO 
 RMS     Displacement     0.018789     0.001200     NO 
--
 Maximum Force            0.000530     0.000450     NO 
 RMS     Force            0.000087     0.000300     YES
 Maximum Displacement     0.268022     0.001800     NO 
 RMS     Displacement     0.026751     0.001200     NO 
--
 Maximum Force            0.000268     0.000450     YES
 RMS     Force            0.000051     0.000300     YES
 Maximum Displacement     0.268678     0.001800     NO 
 RMS     Displacement     0.020944     0.001200     NO 

The above command grew tedious when I wanted to monitor more than a couple jobs, hence I made an alias in the .bashrc file in my home directory. This way I only had to type the alias and not the entire grep line.

# extracts geometry convergence criteria
alias grepmax='grep -A3 -i "maximum force"'

# extracts time stamps for each CCSD gradient calc
alias grepccsd='grep "Leave Link  106"'

# extracts the number of steps taken during a geometry opt, IRC, or PES scan
alias grepstep='grep "Step number"'

# extracts the rotational constants (in GHz)
alias greprot='grep "Rotational constants"'

# extracts the harmonic vibrational frequencies (3 columns)
alias grepfreq='grep "Frequencies"'

# extracts the G3 energy (at 0 K and at finite T, but not the enthalpy or free energy)
alias grepg3='grep "G3(0 K)"'

G03 failing with "end of file in zsymb"

I recently came across an error I had not seen before while running Gaussian03. Right after the input file is read was the line,

End of file in ZSymb.

I had deleted one too many blank lines after the geometry input (G03 needs at least one), and adding a new line back in at the end fixed this right up.

radeon 7xxx video cards throttling

I have several rigs with 2 x 7950 or 2 x 7970 and on some of them (m4a79t + 7950 and m5a97 r2.0 + 7950) the gpu and memory clock is throttled under high load. After some searching around I found this utility that enables the cards to increase the power consumption of each card (gcc and the amd adl-sdk are required):

https://bitcointalk.org/index.php?topic=8384.0

I have included the code here for the impatient.

#include <iostream>
#include <cstdlib>
#include <adl_sdk.h>

using namespace std;

extern "C"
{
    int ADL_Main_Control_Create (ADL_MAIN_MALLOC_CALLBACK, int);
    int ADL_Adapter_NumberOfAdapters_Get(int *);
    int ADL_Overdrive5_PowerControl_Set(int, int);
    int ADL_Overdrive5_PowerControl_Get(int, int *, int *);
}

void* __stdcall Alloc ( int iSize )
{
    void* lpBuffer = malloc ( iSize );
    return lpBuffer;
}

void __stdcall ADL_Main_Memory_Free ( void** lpBuffer )
{
    if ( NULL != *lpBuffer )
    {
        free ( *lpBuffer );
        *lpBuffer = NULL;
    }
}

int main()
{
        int adapters, a=99, b=99;
        if(ADL_Main_Control_Create (Alloc, 1) != ADL_OK)
        {
                cout << "ADL initialization error!" << endl;
                return -1;
        }
        
        if(ADL_Adapter_NumberOfAdapters_Get(&adapters) != ADL_OK)
        {
                cout << "Cannot get the number of adapters!" << endl;
                return -1;
        }
        cout << "Found " << adapters << " adapters" << endl;
        for(int i=0; i<adapters; i++)
        {
                if(ADL_Overdrive5_PowerControl_Set(i, 10) != ADL_OK)
                {
                        cout << "Failed to set " << i << " power control" << endl;
                        return -1;
                } else { cout << "Value set for " << i << endl; }
                
                if(ADL_Overdrive5_PowerControl_Get(i, &a, &b) != ADL_OK)
                {
                        cout << "Failed to get " << i << " power control" << endl;
                        return -1;
                }
                cout << "result: " << a << "%, b: " << b << endl;
        }
        return 0;
}

The key line here is if(ADL_Overdrive5_PowerControl_Set(i, 10) != ADL_OK), and you can change the 10 to any integer up to 20. In my case 5 didn't quite work, so I had to use 10. Then to compile it you use g++, and run it using the 2nd line.

# g++ -DLINUX -o powercontrol powercontrol.cpp -latiadlxx

# ./powercontrol

Found 12 adapters

Value set for 0

result: 10%, b: 0

Value set for 1

result: 10%, b: 0

Value set for 2

result: 10%, b: 0

Value set for 3

result: 10%, b: 0

Value set for 4

result: 10%, b: 0

Value set for 5

result: 10%, b: 0

Value set for 6

result: 10%, b: 0

Value set for 7

result: 10%, b: 0

Value set for 8

result: 10%, b: 0

Value set for 9

result: 10%, b: 0

Value set for 10

result: 10%, b: 0

Value set for 11

result: 10%, b: 0