jmbr

/*
 * Example: spy("foobar.ppm", A);
 */
int spy(std::string const& ppmfile, arma::mat const& M) {
  ofstream ofs(ppmfile);

  if (!ofs.is_open())
    return -1;

  ofs << "P3\n" << M.n_rows << " " << M.n_cols << "\n1\n";

jmbr

#include <cstdlib>

#include <iostream>

#include <SuiteSparseQR.hpp>

int main(int argc, char* argv[]) {
  cholmod_common common;
  cholmod_sparse *A;
  cholmod_dense *x, *b, *residual;

jmbr

This file goes in /usr/lib/gnome-flashback/

#! /bin/sh
exec gnome-session --session=gnome-flashback-stumpwm --disable-acceleration-check "$@"

jmbr

	.text
	.align 4,0x90
	.globl __Z21matrix_vector_productPKdPd
__Z21matrix_vector_productPKdPd:
LFB18:
	movsd	(%rdi), %xmm0
	movsd	8(%rdi), %xmm4
	movapd	%xmm0, %xmm5
	movsd	16(%rdi), %xmm3
	mulsd	%xmm0, %xmm5

jmbr

	.text
	.align 4,0x90
	.globl __Z21matrix_vector_productPKdPd
__Z21matrix_vector_productPKdPd:
LFB18:
	vmovsd	8(%rdi), %xmm2
	vmovsd	(%rdi), %xmm1
	vmulsd	%xmm2, %xmm2, %xmm3
	vmovsd	16(%rdi), %xmm0
	vmovsd	32(%rdi), %xmm6

jmbr

#!/bin/sh

sbcl --eval "(ql:quickload '(:swank :cl-mpi))" \
     --eval "(defun toplevel () \
               (push #'mpi:mpi-finalize *exit-hooks*) \
               (mpi:mpi-init) \
               (let ((port (+ swank::default-server-port (mpi:mpi-comm-rank)))) \
                 (swank:create-server :port port :dont-close t)) \
               (sb-impl::toplevel-init))" \
     --eval "(save-lisp-and-die \"mpisbcl\" :executable t :toplevel #'toplevel)"

jmbr

;;; StumpWM initialization file.

(ql:quickload "swank")

(in-package :stumpwm)

(setf *window-border-style* :none
      *resize-hides-windows* nil)

;;; Redirect output to ~/.stumpwm.d/stumpwm.log

jmbr

reset

load '~/gnuplot-colorbrewer/qualitative/Set2.plt' # Optional

set terminal push
set terminal epslatex size 3.22in, 2.255in
set output "fig-example.tex"

unset key
set border 3

jmbr

import numpy as np
import mdtraj as md
import tqdm


def compute_distance_matrix(trajectory: md.Trajectory) -> np.ndarray:
    """Compute distance matrix.

    """
    topology = trajectory.topology

jmbr

from typing import Tuple

import numpy as np
import scipy.spatial


DEFAULT_NUM_EIGENPAIRS: int = 10 + 1


def diffusion_maps(points: np.ndarray, epsilon2: float,