andersx

\begin{figure}
    \begin{center}
        \includegraphics[width=8.3cm]{my_figure.pdf}
        \caption{This is my figure.}
    \end{center}
\end{figure} 

andersx

import openbabel as ob

# Standard openbabel molecule load
conv = ob.OBConversion()
conv.SetInAndOutFormats('xyz','xyz')
mol = obOBMol()
conv.ReadFile(mol,'my_mol.xyz')

# Define constraints
constraints = ob.OBFFConstraints()

andersx

from fragbuilder import Peptide

# Create a peptide object with the sequence
# glycine-glycine-glycine.
sequence = "GGG"
pep = Peptide(sequence)

# Define a list of angles.
angles = range(-180, 180, 60)

andersx

all: main

main: funclib.o getch_linux.o rovarsprak.c
    gcc -O3 -Wall --pedantic -o main rovarsprak.c funclib.o getch_linux.o

funclib.o: funclib.c funclib.h
    gcc -c -O3 -Wall --pedantic funclib.c -o funclib.o

getch_linux.o: getch_linux.c getch_linux.h
    gcc -c -O3 -Wall --pedantic getch_linux.c -o getch_linux.o

andersx

* water dimer test case for DFTB3 (D3RD HBON)
* DFTB3 single point + gradient.

bomlev 0
! prnlev 7

if ?SCCDFTB .NE. 1 then
  echo "Test NOT Performed."
  STOP
endif

andersx

! Variable declaration:
! =========================
!
! 1) Pythonic naming is used. See: http://legacy.python.org/dev/peps/pep-0008/#naming-conventions
! 2) In brief, this means "lowercase" or "lower_case_with_underscores" are acceptable examples.
! 3) Use descriptive naming.
! 4) Use of abbreviations is discouraged, unless they are very standard. 
!     - E.g. "kcal" for kilocalories is acceptable.
!     - E.g "http" for hypertext transfer protocol is acceptable.
!     - E.g "disp_ver" instead of, say, dispersion version is not acceptable. 

andersx

 $contrl 
    nprint=-5 
    runtyp=gradient 
    ispher=-1 
    maxit=50 
 $end
 

 $system 
    mwords=40 

andersx

// Approximation for EXP(x), only valid for -126.0f < x < 0.0f.
static inline __m256 _mm256_expfast_ps(const __m256 &q) {

    const __m256 INVLOG_2 = _mm256_set1_ps(1.442695040f);
    const __m256 BIT_SHIFT = _mm256_set1_ps(8388608);
    const __m256 ONE = _mm256_set1_ps(1.0f);

    const __m256 C1 = _mm256_set1_ps(121.2740838f);
    const __m256 C2 = _mm256_set1_ps(27.7280233f);
    const __m256 C3 = _mm256_set1_ps(4.84252568f);

andersx

// Approximation for EXP(x) -- very fast, but not super accurate
static inline __m256 _mm256_expfaster_ps(const __m256 &q) {

    const __m256 C1 = _mm256_set1_ps(1064872507.1541044f);
    const __m256 C2 = _mm256_set1_ps(12102203.161561485f);

    return _mm256_castsi256_ps(_mm256_cvttps_epi32(_mm256_fmadd_ps(C2, q, C1)));
}

andersx

#!/bin/bash

# Input pdbfile, force field key, optimization convergence
PDB=$1
FF=$2
CONV=$3

TINKERBIN=/home/andersx/programs/tinker/bin