ad few more manual updates of outdated, mistyped or no longer available URLs

src/MISC/dump_xtc.cpp

@@ -14,7 +14,7 @@
 /* ----------------------------------------------------------------------
    Contributing authors: Naveen Michaud-Agrawal (Johns Hopkins U)
                          open-source XDR routines from
-                           Frans van Hoesel (http://md.chem.rug.nl/hoesel)
+                           Frans van Hoesel (https://www.rug.nl/staff/f.h.j.van.hoesel/)
                            are included in this file
                          Axel Kohlmeyer (Temple U)
                            port to platforms without XDR support

src/RIGID/fix_ehex.cpp

@@ -16,7 +16,7 @@
 
    This source file implements the asymmetric version of the enhanced heat
    exchange (eHEX/a) algorithm. The paper is available for download on
-   arXiv: http://arxiv.org/pdf/1507.07081.pdf.
+   arXiv: https://arxiv.org/pdf/1507.07081.pdf.
 
    This file is based on fix_heat.cpp written by Paul Crozier (SNL)
    which implements the heat exchange (HEX) algorithm.

src/USER-PHONON/dynamical_matrix.cpp

@@ -457,7 +457,7 @@ void DynamicalMatrix::dynmat_clear(double **dynmat)
 void DynamicalMatrix::convert_units(const char *style)
 {
     // physical constants from:
-    // http://physics.nist.gov/cuu/Constants/Table/allascii.txt
+    // https://physics.nist.gov/cuu/Constants/Table/allascii.txt
     // using thermochemical calorie = 4.184 J
 
     if (strcmp(style,"lj") == 0) {

src/USER-PHONON/third_order.cpp

@@ -451,7 +451,7 @@ void ThirdOrder::force_clear()
 void ThirdOrder::convert_units(const char *style)
 {
   // physical constants from:
-  // http://physics.nist.gov/cuu/Constants/Table/allascii.txt
+  // https://physics.nist.gov/cuu/Constants/Table/allascii.txt
   // using thermochemical calorie = 4.184 J
 
   if (strcmp(style,"lj") == 0) {

src/USER-SMD/pair_smd_triangulated_surface.cpp

@@ -517,7 +517,7 @@ double PairTriSurf::memory_usage() {
  % The algorithm is based on
  % "David Eberly, 'Distance Between Point and Triangle in 3D',
  % Geometric Tools, LLC, (1999)"
- % http:\\www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf
+ % https://www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf
  %
  %        ^t
  %  \     |
@@ -739,7 +739,7 @@ double PairTriSurf::memory_usage() {
  * % The algorithm is based on
  % "David Eberly, 'Distance Between Point and Triangle in 3D',
  % Geometric Tools, LLC, (1999)"
- % http:\\www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf
+ % https://www.geometrictools.com/Documentation/DistancePoint3Triangle3.pdf
  */
 
 void PairTriSurf::PointTriangleDistance(const Vector3d sourcePosition, const Vector3d TRI0, const Vector3d TRI1,

src/USER-UEF/uef_utils.cpp

@@ -15,11 +15,11 @@
 
    This class contains functions to calculate the evolution of the periodic
    simulation box under elongational flow as described by Matthew Dobson
-   in the arXiv preprint at http://arxiv.org/abs/1408.7078
+   in the arXiv preprint at https://arxiv.org/abs/1408.7078
 
    Additionally, there are methods to do a lattice reduction to further
    reduce the simulation box using the method of Igor Semaev at
-   http://link.springer.com/chapter/10.1007%2F3-540-44670-2_13
+   https://link.springer.com/chapter/10.1007%2F3-540-44670-2_13
 */
 
 #include <cmath>

src/kspace.cpp

@@ -418,10 +418,9 @@ void KSpace::lamda2xvector(double *lamda, double *v)
 /* ----------------------------------------------------------------------
    convert a sphere in box coords to an ellipsoid in lamda (0-1)
    coords and return the tight (axis-aligned) bounding box, does not
-   preserve vector magnitude
+   preserve vector magnitude see:
-   see http://www.loria.fr/~shornus/ellipsoid-bbox.html and
+   http://www.loria.fr/~shornus/ellipsoid-bbox.html (no longer online) and
-   http://yiningkarlli.blogspot.com/2013/02/
+   https://yiningkarlli.blogspot.com/2013/02/bounding-boxes-for-ellipsoidsfigure.html
-     bounding-boxes-for-ellipsoidsfigure.html
 ------------------------------------------------------------------------- */
 
 void KSpace::kspacebbox(double r, double *b)

src/math_extra.cpp

@@ -453,7 +453,7 @@ void inertia_line(double length, double theta, double mass, double *inertia)
 /* ----------------------------------------------------------------------
    compute space-frame inertia tensor of a triangle
    v0,v1,v2 = 3 vertices of triangle
-   from http://en.wikipedia.org/wiki/Inertia_tensor_of_triangle
+   from https://en.wikipedia.org/wiki/List_of_moments_of_inertia
    inertia tensor = a/24 (v0^2 + v1^2 + v2^2 + (v0+v1+v2)^2) I - a Vt S V
    a = 2*area of tri = |(v1-v0) x (v2-v0)|
    I = 3x3 identity matrix

src/min.cpp

@@ -16,7 +16,7 @@
                         improved CG and backtrack ls, added quadratic ls
    Sources: Numerical Recipes frprmn routine
             "Conjugate Gradient Method Without the Agonizing Pain" by
-            JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
+            JR Shewchuk, https://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf
 ------------------------------------------------------------------------- */
 
 #include "min.h"

src/min_linesearch.cpp

@@ -18,7 +18,7 @@
                         added forcezero ls
    Sources: Numerical Recipes frprmn routine
             "Conjugate Gradient Method Without the Agonizing Pain" by
-            JR Shewchuk, http://www-2.cs.cmu.edu/~jrs/jrspapers.html#cg
+            JR Shewchuk, https://www.cs.cmu.edu/~quake-papers/painless-conjugate-gradient.pdf
 ------------------------------------------------------------------------- */
 
 #include "min_linesearch.h"

src/update.cpp

@@ -124,7 +124,7 @@ void Update::init()
 void Update::set_units(const char *style)
 {
   // physical constants from:
-  // http://physics.nist.gov/cuu/Constants/Table/allascii.txt
+  // https://physics.nist.gov/cuu/Constants/Table/allascii.txt
   // using thermochemical calorie = 4.184 J
 
   double dt_old = dt;