From 7a34d2901406f89217843fcf725ea237d8b66cde Mon Sep 17 00:00:00 2001 From: Daniele Rapetti <5535617+Iximiel@users.noreply.github.com> Date: Wed, 29 Nov 2023 11:12:00 +0100 Subject: [PATCH] rmoved the old pycv tests --- regtest/pycv/.gitignore | 1 - regtest/pycv/Makefile | 2 - regtest/pycv/rt-1/Makefile | 1 - regtest/pycv/rt-1/colvar.out.reference | 5 - regtest/pycv/rt-1/config | 4 - regtest/pycv/rt-1/forces.reference | 24 - regtest/pycv/rt-1/plumed.dat | 10 - regtest/pycv/rt-1/pycv.py | 18 - regtest/pycv/rt-1/traj.xyz | 24 - regtest/pycv/rt-2/GRAD_cv1.reference | 61 -- regtest/pycv/rt-2/GRAD_cv1a.reference | 61 -- regtest/pycv/rt-2/Makefile | 1 - regtest/pycv/rt-2/colvar.out.reference | 5 - regtest/pycv/rt-2/config | 3 - regtest/pycv/rt-2/distcv.py | 28 - regtest/pycv/rt-2/forces.reference | 24 - regtest/pycv/rt-2/plumed.dat | 13 - regtest/pycv/rt-2/traj.xyz | 24 - regtest/pycv/rt-3/Makefile | 1 - regtest/pycv/rt-3/colvar.out.reference | 5 - regtest/pycv/rt-3/config | 3 - regtest/pycv/rt-3/distcv.py | 28 - regtest/pycv/rt-3/plumed.dat | 12 - regtest/pycv/rt-3/traj.xyz | 24 - regtest/pycv/rt-f1/Makefile | 1 - regtest/pycv/rt-f1/colvar.out.reference | 5 - regtest/pycv/rt-f1/config | 4 - regtest/pycv/rt-f1/dAB2_grad.reference | 5 - regtest/pycv/rt-f1/dAB2n_grad.reference | 5 - regtest/pycv/rt-f1/plumed.dat | 15 - regtest/pycv/rt-f1/pythonfunction.py | 8 - regtest/pycv/rt-f1/traj.xyz | 24 - regtest/pycv/rt-f2/COLVAR.reference | 12 - regtest/pycv/rt-f2/Makefile | 1 - regtest/pycv/rt-f2/config | 4 - regtest/pycv/rt-f2/forces.reference | 550 ------------------ regtest/pycv/rt-f2/plumed.dat | 29 - regtest/pycv/rt-f2/pythonfunction.py | 25 - regtest/pycv/rt-jax1/Makefile | 1 - regtest/pycv/rt-jax1/colvar.out.reference | 5 - regtest/pycv/rt-jax1/config | 5 - regtest/pycv/rt-jax1/forces.reference | 24 - regtest/pycv/rt-jax1/jaxcv.py | 17 - regtest/pycv/rt-jax1/plumed.dat | 13 - regtest/pycv/rt-jax1/traj.xyz | 24 - regtest/pycv/rt-jax2/Makefile | 1 - regtest/pycv/rt-jax2/colvar.out.reference | 5 - regtest/pycv/rt-jax2/config | 5 - regtest/pycv/rt-jax2/jaxcv.py | 22 - regtest/pycv/rt-jax2/plumed.dat | 16 - regtest/pycv/rt-jax2/traj.xyz | 24 - regtest/pycv/rt-jax3/COLVAR.reference | 31 - regtest/pycv/rt-jax3/GRADIENT_r.reference | 541 ----------------- regtest/pycv/rt-jax3/Makefile | 1 - regtest/pycv/rt-jax3/arc3.xyz | 150 ----- regtest/pycv/rt-jax3/config | 7 - regtest/pycv/rt-jax3/curvature.py | 36 -- regtest/pycv/rt-jax3/plumed.dat | 12 - regtest/pycv/rt-multi-1/Makefile | 1 - regtest/pycv/rt-multi-1/colvar.out.reference | 5 - regtest/pycv/rt-multi-1/config | 4 - regtest/pycv/rt-multi-1/distcv.py | 45 -- regtest/pycv/rt-multi-1/plumed.dat | 14 - regtest/pycv/rt-multi-1/traj.xyz | 24 - regtest/pycv/rt-multi-2-jax/Makefile | 1 - .../pycv/rt-multi-2-jax/colvar.out.reference | 5 - regtest/pycv/rt-multi-2-jax/config | 5 - regtest/pycv/rt-multi-2-jax/distcv.py | 19 - regtest/pycv/rt-multi-2-jax/plumed.dat | 17 - regtest/pycv/rt-multi-2-jax/traj.xyz | 24 - regtest/pycv/rt-pbc/Makefile | 1 - regtest/pycv/rt-pbc/colvar.reference | 5 - regtest/pycv/rt-pbc/config | 4 - regtest/pycv/rt-pbc/forces.reference | 24 - regtest/pycv/rt-pbc/plumed.dat | 15 - regtest/pycv/rt-pbc/pycv.py | 18 - regtest/pycv/rt-pbc/traj.xyz | 24 - 77 files changed, 2265 deletions(-) delete mode 100644 regtest/pycv/.gitignore delete mode 100644 regtest/pycv/Makefile delete mode 100644 regtest/pycv/rt-1/Makefile delete mode 100644 regtest/pycv/rt-1/colvar.out.reference delete mode 100644 regtest/pycv/rt-1/config delete mode 100644 regtest/pycv/rt-1/forces.reference delete mode 100644 regtest/pycv/rt-1/plumed.dat delete mode 100644 regtest/pycv/rt-1/pycv.py delete mode 100644 regtest/pycv/rt-1/traj.xyz delete mode 100644 regtest/pycv/rt-2/GRAD_cv1.reference delete mode 100644 regtest/pycv/rt-2/GRAD_cv1a.reference delete mode 100644 regtest/pycv/rt-2/Makefile delete mode 100644 regtest/pycv/rt-2/colvar.out.reference delete mode 100644 regtest/pycv/rt-2/config delete mode 100644 regtest/pycv/rt-2/distcv.py delete mode 100644 regtest/pycv/rt-2/forces.reference delete mode 100644 regtest/pycv/rt-2/plumed.dat delete mode 100644 regtest/pycv/rt-2/traj.xyz delete mode 100644 regtest/pycv/rt-3/Makefile delete mode 100644 regtest/pycv/rt-3/colvar.out.reference delete mode 100644 regtest/pycv/rt-3/config delete mode 100644 regtest/pycv/rt-3/distcv.py delete mode 100644 regtest/pycv/rt-3/plumed.dat delete mode 100644 regtest/pycv/rt-3/traj.xyz delete mode 100644 regtest/pycv/rt-f1/Makefile delete mode 100644 regtest/pycv/rt-f1/colvar.out.reference delete mode 100644 regtest/pycv/rt-f1/config delete mode 100644 regtest/pycv/rt-f1/dAB2_grad.reference delete mode 100644 regtest/pycv/rt-f1/dAB2n_grad.reference delete mode 100644 regtest/pycv/rt-f1/plumed.dat delete mode 100644 regtest/pycv/rt-f1/pythonfunction.py delete mode 100644 regtest/pycv/rt-f1/traj.xyz delete mode 100644 regtest/pycv/rt-f2/COLVAR.reference delete mode 100644 regtest/pycv/rt-f2/Makefile delete mode 100644 regtest/pycv/rt-f2/config delete mode 100644 regtest/pycv/rt-f2/forces.reference delete mode 100644 regtest/pycv/rt-f2/plumed.dat delete mode 100644 regtest/pycv/rt-f2/pythonfunction.py delete mode 100644 regtest/pycv/rt-jax1/Makefile delete mode 100644 regtest/pycv/rt-jax1/colvar.out.reference delete mode 100644 regtest/pycv/rt-jax1/config delete mode 100644 regtest/pycv/rt-jax1/forces.reference delete mode 100644 regtest/pycv/rt-jax1/jaxcv.py delete mode 100644 regtest/pycv/rt-jax1/plumed.dat delete mode 100644 regtest/pycv/rt-jax1/traj.xyz delete mode 100644 regtest/pycv/rt-jax2/Makefile delete mode 100644 regtest/pycv/rt-jax2/colvar.out.reference delete mode 100644 regtest/pycv/rt-jax2/config delete mode 100644 regtest/pycv/rt-jax2/jaxcv.py delete mode 100644 regtest/pycv/rt-jax2/plumed.dat delete mode 100644 regtest/pycv/rt-jax2/traj.xyz delete mode 100644 regtest/pycv/rt-jax3/COLVAR.reference delete mode 100644 regtest/pycv/rt-jax3/GRADIENT_r.reference delete mode 100644 regtest/pycv/rt-jax3/Makefile delete mode 100644 regtest/pycv/rt-jax3/arc3.xyz delete mode 100644 regtest/pycv/rt-jax3/config delete mode 100644 regtest/pycv/rt-jax3/curvature.py delete mode 100644 regtest/pycv/rt-jax3/plumed.dat delete mode 100644 regtest/pycv/rt-multi-1/Makefile delete mode 100644 regtest/pycv/rt-multi-1/colvar.out.reference delete mode 100644 regtest/pycv/rt-multi-1/config delete mode 100644 regtest/pycv/rt-multi-1/distcv.py delete mode 100644 regtest/pycv/rt-multi-1/plumed.dat delete mode 100644 regtest/pycv/rt-multi-1/traj.xyz delete mode 100644 regtest/pycv/rt-multi-2-jax/Makefile delete mode 100644 regtest/pycv/rt-multi-2-jax/colvar.out.reference delete mode 100644 regtest/pycv/rt-multi-2-jax/config delete mode 100644 regtest/pycv/rt-multi-2-jax/distcv.py delete mode 100644 regtest/pycv/rt-multi-2-jax/plumed.dat delete mode 100644 regtest/pycv/rt-multi-2-jax/traj.xyz delete mode 100644 regtest/pycv/rt-pbc/Makefile delete mode 100644 regtest/pycv/rt-pbc/colvar.reference delete mode 100644 regtest/pycv/rt-pbc/config delete mode 100644 regtest/pycv/rt-pbc/forces.reference delete mode 100644 regtest/pycv/rt-pbc/plumed.dat delete mode 100644 regtest/pycv/rt-pbc/pycv.py delete mode 100644 regtest/pycv/rt-pbc/traj.xyz diff --git a/regtest/pycv/.gitignore b/regtest/pycv/.gitignore deleted file mode 100644 index ba0430d26c..0000000000 --- a/regtest/pycv/.gitignore +++ /dev/null @@ -1 +0,0 @@ -__pycache__/ \ No newline at end of file diff --git a/regtest/pycv/Makefile b/regtest/pycv/Makefile deleted file mode 100644 index 42480767ae..0000000000 --- a/regtest/pycv/Makefile +++ /dev/null @@ -1,2 +0,0 @@ -include ../scripts/module.make - diff --git a/regtest/pycv/rt-1/Makefile b/regtest/pycv/rt-1/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-1/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-1/colvar.out.reference b/regtest/pycv/rt-1/colvar.out.reference deleted file mode 100644 index cb855c936e..0000000000 --- a/regtest/pycv/rt-1/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1 cv1n - 0.000000 5.000000 5.000000 - 1.000000 8.660254 8.660254 - 2.000000 11.180340 11.180340 - 3.000000 8.660254 8.660254 diff --git a/regtest/pycv/rt-1/config b/regtest/pycv/rt-1/config deleted file mode 100644 index 6839ec1758..0000000000 --- a/regtest/pycv/rt-1/config +++ /dev/null @@ -1,4 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -plumed_modules=pycv diff --git a/regtest/pycv/rt-1/forces.reference b/regtest/pycv/rt-1/forces.reference deleted file mode 100644 index 2d2bbe7469..0000000000 --- a/regtest/pycv/rt-1/forces.reference +++ /dev/null @@ -1,24 +0,0 @@ -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 diff --git a/regtest/pycv/rt-1/plumed.dat b/regtest/pycv/rt-1/plumed.dat deleted file mode 100644 index 8fe61c11c7..0000000000 --- a/regtest/pycv/rt-1/plumed.dat +++ /dev/null @@ -1,10 +0,0 @@ -# LOAD FILE=PythonCV.dylib - -cv1: PYTHONCV ATOMS=1,4 IMPORT=pycv FUNCTION=cv1 - -cv1n: DISTANCE ATOMS=1,4 - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-1/pycv.py b/regtest/pycv/rt-1/pycv.py deleted file mode 100644 index 5bb95959ea..0000000000 --- a/regtest/pycv/rt-1/pycv.py +++ /dev/null @@ -1,18 +0,0 @@ -# This is only a partial example. This function does not compute the -# gradient, so it is useless for biasing. See the other regression -# tests for how to auto-grad. - -# And, of course, one should not call slow functions (such as print) -# in the CV calculation. - -import numpy as np -log=open("pycv.log","w") - -print("Imported.",file=log) - -def cv1(x): - print(x,file=log) # But don't - d = x[0,:]-x[1,:] - d2 = np.dot(d,d) - # If computing a gradient, return it as a 2nd return value. - return np.sqrt(d2) diff --git a/regtest/pycv/rt-1/traj.xyz b/regtest/pycv/rt-1/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-1/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-2/GRAD_cv1.reference b/regtest/pycv/rt-2/GRAD_cv1.reference deleted file mode 100644 index 596f252fac..0000000000 --- a/regtest/pycv/rt-2/GRAD_cv1.reference +++ /dev/null @@ -1,61 +0,0 @@ -#! FIELDS time parameter cv1 - 0.000000 0 0.0000 - 0.000000 1 -1.0000 - 0.000000 2 0.0000 - 0.000000 3 0.0000 - 0.000000 4 1.0000 - 0.000000 5 0.0000 - 0.000000 6 0.0000 - 0.000000 7 0.0000 - 0.000000 8 0.0000 - 0.000000 9 0.0000 - 0.000000 10 -5.0000 - 0.000000 11 0.0000 - 0.000000 12 0.0000 - 0.000000 13 0.0000 - 0.000000 14 0.0000 - 1.000000 0 0.5774 - 1.000000 1 -0.5774 - 1.000000 2 -0.5774 - 1.000000 3 -0.5774 - 1.000000 4 0.5774 - 1.000000 5 0.5774 - 1.000000 6 -2.8868 - 1.000000 7 2.8868 - 1.000000 8 2.8868 - 1.000000 9 2.8868 - 1.000000 10 -2.8868 - 1.000000 11 -2.8868 - 1.000000 12 2.8868 - 1.000000 13 -2.8868 - 1.000000 14 -2.8868 - 2.000000 0 0.8944 - 2.000000 1 -0.4472 - 2.000000 2 0.0000 - 2.000000 3 -0.8944 - 2.000000 4 0.4472 - 2.000000 5 0.0000 - 2.000000 6 -8.9443 - 2.000000 7 4.4721 - 2.000000 8 0.0000 - 2.000000 9 4.4721 - 2.000000 10 -2.2361 - 2.000000 11 0.0000 - 2.000000 12 0.0000 - 2.000000 13 0.0000 - 2.000000 14 0.0000 - 3.000000 0 0.5774 - 3.000000 1 -0.5774 - 3.000000 2 0.5774 - 3.000000 3 -0.5774 - 3.000000 4 0.5774 - 3.000000 5 -0.5774 - 3.000000 6 -2.8868 - 3.000000 7 2.8868 - 3.000000 8 -2.8868 - 3.000000 9 2.8868 - 3.000000 10 -2.8868 - 3.000000 11 2.8868 - 3.000000 12 -2.8868 - 3.000000 13 2.8868 - 3.000000 14 -2.8868 diff --git a/regtest/pycv/rt-2/GRAD_cv1a.reference b/regtest/pycv/rt-2/GRAD_cv1a.reference deleted file mode 100644 index 430c2e25da..0000000000 --- a/regtest/pycv/rt-2/GRAD_cv1a.reference +++ /dev/null @@ -1,61 +0,0 @@ -#! FIELDS time parameter cv1a - 0.000000 0 0.0000 - 0.000000 1 -1.0000 - 0.000000 2 0.0000 - 0.000000 3 0.0000 - 0.000000 4 1.0000 - 0.000000 5 0.0000 - 0.000000 6 0.0000 - 0.000000 7 0.0000 - 0.000000 8 0.0000 - 0.000000 9 0.0000 - 0.000000 10 -5.0000 - 0.000000 11 0.0000 - 0.000000 12 0.0000 - 0.000000 13 0.0000 - 0.000000 14 0.0000 - 1.000000 0 0.5774 - 1.000000 1 -0.5774 - 1.000000 2 -0.5774 - 1.000000 3 -0.5774 - 1.000000 4 0.5774 - 1.000000 5 0.5774 - 1.000000 6 -2.8868 - 1.000000 7 2.8868 - 1.000000 8 2.8868 - 1.000000 9 2.8868 - 1.000000 10 -2.8868 - 1.000000 11 -2.8868 - 1.000000 12 2.8868 - 1.000000 13 -2.8868 - 1.000000 14 -2.8868 - 2.000000 0 0.8944 - 2.000000 1 -0.4472 - 2.000000 2 0.0000 - 2.000000 3 -0.8944 - 2.000000 4 0.4472 - 2.000000 5 0.0000 - 2.000000 6 -8.9443 - 2.000000 7 4.4721 - 2.000000 8 0.0000 - 2.000000 9 4.4721 - 2.000000 10 -2.2361 - 2.000000 11 0.0000 - 2.000000 12 0.0000 - 2.000000 13 0.0000 - 2.000000 14 0.0000 - 3.000000 0 0.5774 - 3.000000 1 -0.5774 - 3.000000 2 0.5774 - 3.000000 3 -0.5774 - 3.000000 4 0.5774 - 3.000000 5 -0.5774 - 3.000000 6 -2.8868 - 3.000000 7 2.8868 - 3.000000 8 -2.8868 - 3.000000 9 2.8868 - 3.000000 10 -2.8868 - 3.000000 11 2.8868 - 3.000000 12 -2.8868 - 3.000000 13 2.8868 - 3.000000 14 -2.8868 diff --git a/regtest/pycv/rt-2/Makefile b/regtest/pycv/rt-2/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-2/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-2/colvar.out.reference b/regtest/pycv/rt-2/colvar.out.reference deleted file mode 100644 index 12410d685a..0000000000 --- a/regtest/pycv/rt-2/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1 cv1a @2.bias @2.force2 - 0.000000 5.000000 5.000000 -5.000000 1.000000 - 1.000000 8.660254 8.660254 -8.660254 1.000000 - 2.000000 11.180340 11.180340 -11.180340 1.000000 - 3.000000 8.660254 8.660254 -8.660254 1.000000 diff --git a/regtest/pycv/rt-2/config b/regtest/pycv/rt-2/config deleted file mode 100644 index 965c0a2a98..0000000000 --- a/regtest/pycv/rt-2/config +++ /dev/null @@ -1,3 +0,0 @@ -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -plumed_modules=pycv diff --git a/regtest/pycv/rt-2/distcv.py b/regtest/pycv/rt-2/distcv.py deleted file mode 100644 index e87e004e08..0000000000 --- a/regtest/pycv/rt-2/distcv.py +++ /dev/null @@ -1,28 +0,0 @@ -import numpy as np - -# In reality one should not log stuff here... -log=open("log.txt","w",1) - -print("At import",file=log) - - - -# Define the distance function -def dist(x): - print("In dist()",file=log) - print(x,file=log) - r = x[0,:]-x[1,:] - d2 = np.dot(r,r) - return np.sqrt(d2) - -def grad_dist(x): - print("In grad_dist()",file=log) - d = dist(x) - r = x[0,:]-x[1,:] - g = r/d - return np.array([g,-g]) - -# The CV function actually called -def cv(x): - return dist(x), grad_dist(x) - diff --git a/regtest/pycv/rt-2/forces.reference b/regtest/pycv/rt-2/forces.reference deleted file mode 100644 index 3dcd17b798..0000000000 --- a/regtest/pycv/rt-2/forces.reference +++ /dev/null @@ -1,24 +0,0 @@ -4 - 0.000000 -5.000000 0.000000 -X 0.000000 -1.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 1.000000 0.000000 -4 - -2.886751 -2.886751 -2.886751 -X 0.577350 -0.577350 -0.577350 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.577350 0.577350 0.577350 -4 - -8.944272 -2.236068 0.000000 -X 0.894427 -0.447214 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.894427 0.447214 0.000000 -4 - -2.886751 -2.886751 -2.886751 -X 0.577350 -0.577350 0.577350 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.577350 0.577350 -0.577350 diff --git a/regtest/pycv/rt-2/plumed.dat b/regtest/pycv/rt-2/plumed.dat deleted file mode 100644 index 8456f98160..0000000000 --- a/regtest/pycv/rt-2/plumed.dat +++ /dev/null @@ -1,13 +0,0 @@ - -cv1: PYTHONCV ATOMS=1,4 IMPORT=distcv FUNCTION=cv -cv1a: DISTANCE ATOMS=1,4 - -RESTRAINT AT=0 SLOPE=-1 ARG=cv1 - -DUMPDERIVATIVES ARG=cv1 FILE=GRAD_cv1 FMT=%8.4f -DUMPDERIVATIVES ARG=cv1a FILE=GRAD_cv1a FMT=%8.4f - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-2/traj.xyz b/regtest/pycv/rt-2/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-2/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-3/Makefile b/regtest/pycv/rt-3/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-3/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-3/colvar.out.reference b/regtest/pycv/rt-3/colvar.out.reference deleted file mode 100644 index 07c4b34ec6..0000000000 --- a/regtest/pycv/rt-3/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1 cv2 cv1a cv2a - 0.000000 5.000000 7.071068 5.000000 7.071068 - 1.000000 8.660254 7.071068 8.660254 7.071068 - 2.000000 11.180340 7.071068 11.180340 7.071068 - 3.000000 8.660254 7.071068 8.660254 7.071068 diff --git a/regtest/pycv/rt-3/config b/regtest/pycv/rt-3/config deleted file mode 100644 index 965c0a2a98..0000000000 --- a/regtest/pycv/rt-3/config +++ /dev/null @@ -1,3 +0,0 @@ -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -plumed_modules=pycv diff --git a/regtest/pycv/rt-3/distcv.py b/regtest/pycv/rt-3/distcv.py deleted file mode 100644 index e87e004e08..0000000000 --- a/regtest/pycv/rt-3/distcv.py +++ /dev/null @@ -1,28 +0,0 @@ -import numpy as np - -# In reality one should not log stuff here... -log=open("log.txt","w",1) - -print("At import",file=log) - - - -# Define the distance function -def dist(x): - print("In dist()",file=log) - print(x,file=log) - r = x[0,:]-x[1,:] - d2 = np.dot(r,r) - return np.sqrt(d2) - -def grad_dist(x): - print("In grad_dist()",file=log) - d = dist(x) - r = x[0,:]-x[1,:] - g = r/d - return np.array([g,-g]) - -# The CV function actually called -def cv(x): - return dist(x), grad_dist(x) - diff --git a/regtest/pycv/rt-3/plumed.dat b/regtest/pycv/rt-3/plumed.dat deleted file mode 100644 index 4d1075fb61..0000000000 --- a/regtest/pycv/rt-3/plumed.dat +++ /dev/null @@ -1,12 +0,0 @@ - -cv1: PYTHONCV ATOMS=1,4 IMPORT=distcv FUNCTION=cv -cv2: PYTHONCV ATOMS=1,3 IMPORT=distcv FUNCTION=cv - -cv1a: DISTANCE ATOMS=1,4 -cv2a: DISTANCE ATOMS=1,3 - - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-3/traj.xyz b/regtest/pycv/rt-3/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-3/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-f1/Makefile b/regtest/pycv/rt-f1/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-f1/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-f1/colvar.out.reference b/regtest/pycv/rt-f1/colvar.out.reference deleted file mode 100644 index d94af2bfa7..0000000000 --- a/regtest/pycv/rt-f1/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time dAB dAB2 dAB2n - 0.000000 5.000000 25.000000 25.000000 - 1.000000 8.660254 75.000008 75.000000 - 2.000000 11.180340 125.000000 125.000000 - 3.000000 8.660254 75.000008 75.000000 diff --git a/regtest/pycv/rt-f1/config b/regtest/pycv/rt-f1/config deleted file mode 100644 index 6839ec1758..0000000000 --- a/regtest/pycv/rt-f1/config +++ /dev/null @@ -1,4 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -plumed_modules=pycv diff --git a/regtest/pycv/rt-f1/dAB2_grad.reference b/regtest/pycv/rt-f1/dAB2_grad.reference deleted file mode 100644 index 6b089d9a2f..0000000000 --- a/regtest/pycv/rt-f1/dAB2_grad.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time parameter dAB2 - 0.000000 0 10.00000 - 1.000000 0 17.32051 - 2.000000 0 22.36068 - 3.000000 0 17.32051 diff --git a/regtest/pycv/rt-f1/dAB2n_grad.reference b/regtest/pycv/rt-f1/dAB2n_grad.reference deleted file mode 100644 index 4dd8398f8c..0000000000 --- a/regtest/pycv/rt-f1/dAB2n_grad.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time parameter dAB2n - 0.000000 0 10.00000 - 1.000000 0 17.32051 - 2.000000 0 22.36068 - 3.000000 0 17.32051 diff --git a/regtest/pycv/rt-f1/plumed.dat b/regtest/pycv/rt-f1/plumed.dat deleted file mode 100644 index 9c96949f7b..0000000000 --- a/regtest/pycv/rt-f1/plumed.dat +++ /dev/null @@ -1,15 +0,0 @@ -# LOAD FILE=PythonCV.dylib - -dAB: DISTANCE ATOMS=1,4 - -dAB2: PYTHONFUNCTION ARG=dAB IMPORT=pythonfunction FUNCTION=square PERIODIC=NO - -dAB2n: COMBINE ARG=dAB POWERS=2.0 PERIODIC=NO - -DUMPDERIVATIVES ARG=dAB2 FILE=dAB2_grad FMT=%.5f -DUMPDERIVATIVES ARG=dAB2n FILE=dAB2n_grad FMT=%.5f - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-f1/pythonfunction.py b/regtest/pycv/rt-f1/pythonfunction.py deleted file mode 100644 index 722f9a36f3..0000000000 --- a/regtest/pycv/rt-f1/pythonfunction.py +++ /dev/null @@ -1,8 +0,0 @@ - -import numpy as np - - -def square(x): - return x[0]**2, np.array([2*x[0]]) - - diff --git a/regtest/pycv/rt-f1/traj.xyz b/regtest/pycv/rt-f1/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-f1/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-f2/COLVAR.reference b/regtest/pycv/rt-f2/COLVAR.reference deleted file mode 100644 index 0c60007694..0000000000 --- a/regtest/pycv/rt-f2/COLVAR.reference +++ /dev/null @@ -1,12 +0,0 @@ -#! FIELDS time t1 t2 t3 cc1 cc2 cc3 all -#! SET min_t1 -pi -#! SET max_t1 pi -#! SET min_t2 -pi -#! SET max_t2 pi -#! SET min_t3 -pi -#! SET max_t3 pi - 0.000000 -1.69727 -1.69727 0.25617 2.18345 -0.00000 5.76145 0.80109 - 0.050000 -1.81921 -1.81921 0.29414 2.49031 -0.00000 6.61905 0.96085 - 0.100000 -1.92318 -1.92318 0.32805 2.77543 -0.00000 7.39721 1.10906 - 0.150000 -2.02490 -2.02490 0.36930 3.07533 -0.00000 8.20048 1.26588 - 0.200000 -2.11789 -2.11789 0.41443 3.36757 -0.00000 8.97091 1.41952 diff --git a/regtest/pycv/rt-f2/Makefile b/regtest/pycv/rt-f2/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-f2/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-f2/config b/regtest/pycv/rt-f2/config deleted file mode 100644 index 339c9f6ed1..0000000000 --- a/regtest/pycv/rt-f2/config +++ /dev/null @@ -1,4 +0,0 @@ -type=driver -arg="--plumed plumed.dat --trajectory-stride 10 --timestep 0.005 --ixyz trajectory.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -extra_files="../../trajectories/trajectory.xyz" -plumed_modules=pycv diff --git a/regtest/pycv/rt-f2/forces.reference b/regtest/pycv/rt-f2/forces.reference deleted file mode 100644 index 19b9914bf2..0000000000 --- a/regtest/pycv/rt-f2/forces.reference +++ /dev/null @@ -1,550 +0,0 @@ -108 - -0.017673 0.047772 -0.030099 -X -0.048958 1.204894 -0.005442 -X -0.006141 -0.003009 0.000498 -X -0.006141 -0.003009 0.000498 -X -0.006141 -0.003009 0.000498 -X -0.006141 -0.003009 0.000498 -X -0.030777 -2.854875 -0.022522 -X -0.006842 -0.006147 0.006055 -X -0.006141 -0.003009 0.000498 -X -0.006141 -0.003009 0.000498 -X 0.595226 1.649410 0.046779 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.472503 0.021634 -0.022299 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000701 0.003138 -0.005557 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -108 - -0.080903 0.108540 -0.027638 -X -0.148269 1.187893 0.012784 -X -0.006208 -0.002901 0.000389 -X -0.006208 -0.002901 0.000389 -X -0.006208 -0.002901 0.000389 -X -0.006208 -0.002901 0.000389 -X 0.222310 -2.747665 -0.070647 -X -0.006843 -0.006807 0.007187 -X -0.006208 -0.002901 0.000389 -X -0.006208 -0.002901 0.000389 -X 0.485181 1.536539 0.094032 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.515765 0.043537 -0.038890 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000635 0.003906 -0.006798 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -108 - -0.109043 0.126172 -0.017130 -X -0.211650 1.140171 0.031316 -X -0.006216 -0.003041 0.000213 -X -0.006216 -0.003041 0.000213 -X -0.006216 -0.003041 0.000213 -X -0.006216 -0.003041 0.000213 -X 0.389689 -2.600949 -0.116753 -X -0.005758 -0.007160 0.007797 -X -0.006216 -0.003041 0.000213 -X -0.006216 -0.003041 0.000213 -X 0.414776 1.409162 0.143572 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.549301 0.072906 -0.059628 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.000458 0.004119 -0.007584 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -108 - -0.157705 0.151967 0.005738 -X -0.270665 1.067251 0.048696 -X -0.006213 -0.003240 -0.000008 -X -0.006213 -0.003240 -0.000008 -X -0.006213 -0.003240 -0.000008 -X -0.006213 -0.003240 -0.000008 -X 0.549175 -2.407085 -0.157636 -X -0.004598 -0.007690 0.008565 -X -0.006213 -0.003240 -0.000008 -X -0.006213 -0.003240 -0.000008 -X 0.335428 1.261536 0.191886 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.570448 0.100974 -0.082891 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.001614 0.004450 -0.008573 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -108 - -0.212077 0.174909 0.037168 -X -0.323978 1.008335 0.059776 -X -0.006182 -0.003446 -0.000228 -X -0.006182 -0.003446 -0.000228 -X -0.006182 -0.003446 -0.000228 -X -0.006182 -0.003446 -0.000228 -X 0.678771 -2.215551 -0.178676 -X -0.003198 -0.008238 0.009618 -X -0.006182 -0.003446 -0.000228 -X -0.006182 -0.003446 -0.000228 -X 0.275669 1.103648 0.224130 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.587192 0.127689 -0.103633 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X -0.002983 0.004792 -0.009846 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 diff --git a/regtest/pycv/rt-f2/plumed.dat b/regtest/pycv/rt-f2/plumed.dat deleted file mode 100644 index 0ef88dbf55..0000000000 --- a/regtest/pycv/rt-f2/plumed.dat +++ /dev/null @@ -1,29 +0,0 @@ -# Copy of basic/rt13 - -g1: GROUP ATOMS=1-10 -c1: CENTER ATOMS=g1 - -t1: TORSION ATOMS=1,6,10,15 -t2: TORSION VECTOR1=6,1 AXIS=6,10 VECTOR2=10,15 -t3: TORSION VECTOR1=6,1 AXIS=20,7 VECTOR2=10,c1 - -cc1: PYTHONFUNCTION ARG=t1,t2,t3 IMPORT=pythonfunction FUNCTION=cc1 PERIODIC=NO -cc2: PYTHONFUNCTION ARG=t1,t2,t3 IMPORT=pythonfunction FUNCTION=cc2 PERIODIC=NO -cc3: PYTHONFUNCTION ARG=t1,t2 IMPORT=pythonfunction FUNCTION=cc3 PERIODIC=NO - -# cc1: MATHEVAL ARG=t1,t2,t3 FUNC=x^2+y+0*z+1 PERIODIC=NO -# cc2: MATHEVAL ARG=t1,t2,t3 FUNC=0*x^3+0*y^3+0*z^3 PERIODIC=NO -# cc3: MATHEVAL ARG=t1,t2 FUNC=x^2+y^2 PERIODIC=NO - -all: CUSTOM ARG=t1,t2,t3,cc1,cc2,cc3 VAR=a1,a2,a3,a4,a5,a6 FUNC={ (a1+a2+a3+a4+a5+a6) / 6.0 } PERIODIC=NO - -RESTRAINT ARG=all AT=0 SLOPE=1.0 - -PRINT ... - STRIDE=2 - ARG=t1,t2,t3,cc1,cc2,cc3,all - FILE=COLVAR FMT=%6.5f -... PRINT - -ENDPLUMED - diff --git a/regtest/pycv/rt-f2/pythonfunction.py b/regtest/pycv/rt-f2/pythonfunction.py deleted file mode 100644 index 59cde42464..0000000000 --- a/regtest/pycv/rt-f2/pythonfunction.py +++ /dev/null @@ -1,25 +0,0 @@ -#import jax.numpy as np -from jax import grad,jit - -@jit -def cc1f(xx): - x, y, z = xx - return x**2+y+0*z+1 -cc1g=grad(cc1f) -def cc1(x): return cc1f(x), cc1g(x) - -@jit -def cc2f(xx): - x, y, z = xx - return 0*x**3+0*y**3+0*z**3 -cc2g=grad(cc2f) -def cc2(x): return cc2f(x), cc2g(x) - -@jit -def cc3f(xx): - x, y = xx - return x**2+y**2 -cc3g=grad(cc3f) -def cc3(x): return cc3f(x), cc3g(x) - - diff --git a/regtest/pycv/rt-jax1/Makefile b/regtest/pycv/rt-jax1/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-jax1/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-jax1/colvar.out.reference b/regtest/pycv/rt-jax1/colvar.out.reference deleted file mode 100644 index cb855c936e..0000000000 --- a/regtest/pycv/rt-jax1/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1 cv1n - 0.000000 5.000000 5.000000 - 1.000000 8.660254 8.660254 - 2.000000 11.180340 11.180340 - 3.000000 8.660254 8.660254 diff --git a/regtest/pycv/rt-jax1/config b/regtest/pycv/rt-jax1/config deleted file mode 100644 index a7cc659930..0000000000 --- a/regtest/pycv/rt-jax1/config +++ /dev/null @@ -1,5 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -PLUMED_ALLOW_SKIP_ON_TRAVIS=yes -plumed_modules=pycv diff --git a/regtest/pycv/rt-jax1/forces.reference b/regtest/pycv/rt-jax1/forces.reference deleted file mode 100644 index 2d2bbe7469..0000000000 --- a/regtest/pycv/rt-jax1/forces.reference +++ /dev/null @@ -1,24 +0,0 @@ -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 diff --git a/regtest/pycv/rt-jax1/jaxcv.py b/regtest/pycv/rt-jax1/jaxcv.py deleted file mode 100644 index 33bbfe65cd..0000000000 --- a/regtest/pycv/rt-jax1/jaxcv.py +++ /dev/null @@ -1,17 +0,0 @@ -# Import the JAX library -import jax.numpy as np -from jax import grad, jit - -# Define the distance function -@jit -def dist(x): - d = x[0,:]-x[1,:] - d2 = np.dot(d,d) - return np.sqrt(d2) - -# Use JAX to auto-gradient it -grad_dist = grad(dist) - -# The CV function actually called -def cv1(x): - return dist(x), grad_dist(x) diff --git a/regtest/pycv/rt-jax1/plumed.dat b/regtest/pycv/rt-jax1/plumed.dat deleted file mode 100644 index 74b940653b..0000000000 --- a/regtest/pycv/rt-jax1/plumed.dat +++ /dev/null @@ -1,13 +0,0 @@ -# LOAD FILE=PythonCV.dylib - -cv1: PYTHONCV ATOMS=1,4 IMPORT=jaxcv FUNCTION=cv1 - -cv1n: DISTANCE ATOMS=1,4 - -DUMPDERIVATIVES ARG=cv1 FILE=GRAD_cv1 FMT=%8.4f -DUMPDERIVATIVES ARG=cv1n FILE=GRAD_cv1n FMT=%8.4f - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-jax1/traj.xyz b/regtest/pycv/rt-jax1/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-jax1/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-jax2/Makefile b/regtest/pycv/rt-jax2/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-jax2/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-jax2/colvar.out.reference b/regtest/pycv/rt-jax2/colvar.out.reference deleted file mode 100644 index de85c0d39c..0000000000 --- a/regtest/pycv/rt-jax2/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1 cv1a cv1n @3.bias @3.force2 @4.bias @4.force2 - 0.000000 1.570796 1.570796 1.570796 -1.570796 1.000000 1.570796 1.000000 - 1.000000 0.955317 0.955317 0.955317 -0.955317 1.000000 0.955317 1.000000 - 2.000000 0.463648 0.463648 0.463648 -0.463648 1.000000 0.463648 1.000000 - 3.000000 0.955317 0.955317 0.955317 -0.955317 1.000000 0.955317 1.000000 diff --git a/regtest/pycv/rt-jax2/config b/regtest/pycv/rt-jax2/config deleted file mode 100644 index a7cc659930..0000000000 --- a/regtest/pycv/rt-jax2/config +++ /dev/null @@ -1,5 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -PLUMED_ALLOW_SKIP_ON_TRAVIS=yes -plumed_modules=pycv diff --git a/regtest/pycv/rt-jax2/jaxcv.py b/regtest/pycv/rt-jax2/jaxcv.py deleted file mode 100644 index b5115d0727..0000000000 --- a/regtest/pycv/rt-jax2/jaxcv.py +++ /dev/null @@ -1,22 +0,0 @@ -# Import the JAX library -import jax.numpy as np -from jax import grad, jit - -# Implementation of the angle function. @jit really improves speed -@jit -def angle(x): - r1 = x[0,:]-x[1,:] - r2 = x[2,:]-x[1,:] - - # costheta = np.dot(r1,r2) / np.linalg.norm(r1) / np.linalg.norm(r2) - costheta = np.dot(r1,r2) / np.sqrt(np.dot(r1,r1) * np.dot(r2,r2)) - theta = np.arccos(costheta) - return theta - -# Use JAX to auto-gradient it -grad_angle = grad(angle) - -# The CV function actually called -def cv1(x): - return angle(x), grad_angle(x) - diff --git a/regtest/pycv/rt-jax2/plumed.dat b/regtest/pycv/rt-jax2/plumed.dat deleted file mode 100644 index 86eae6b354..0000000000 --- a/regtest/pycv/rt-jax2/plumed.dat +++ /dev/null @@ -1,16 +0,0 @@ - -cv1: PYTHONCV ATOMS=1,4,3 IMPORT=jaxcv FUNCTION=cv1 -cv1a: ANGLE ATOMS=1,4,3 -cv1n: PYTHONCV ATOMS=1,4,3 IMPORT=jaxcv FUNCTION=cv1 NUMERICAL_DERIVATIVES - -RESTRAINT AT=0 SLOPE=-1 ARG=cv1 -RESTRAINT AT=0 SLOPE=+1 ARG=cv1a - -DUMPDERIVATIVES ARG=cv1 FILE=GRAD_cv1 FMT=%8.4f -DUMPDERIVATIVES ARG=cv1a FILE=GRAD_cv1a FMT=%8.4f -DUMPDERIVATIVES ARG=cv1n FILE=GRAD_cv1n FMT=%8.4f - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-jax2/traj.xyz b/regtest/pycv/rt-jax2/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-jax2/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-jax3/COLVAR.reference b/regtest/pycv/rt-jax3/COLVAR.reference deleted file mode 100644 index 2aeb3e1597..0000000000 --- a/regtest/pycv/rt-jax3/COLVAR.reference +++ /dev/null @@ -1,31 +0,0 @@ -#! FIELDS time r ir - 0.000000 5.0500 0.1980 - 1.000000 5.0500 0.1980 - 2.000000 2.6000 0.3846 - 3.000000 1.8167 0.5505 - 4.000000 1.4500 0.6897 - 5.000000 1.2500 0.8000 - 6.000000 1.1333 0.8824 - 7.000000 1.0643 0.9396 - 8.000000 1.0250 0.9756 - 9.000000 1.0056 0.9945 - 10.000000 1.0000 1.0000 - 11.000000 1.0045 0.9955 - 12.000000 1.0167 0.9836 - 13.000000 1.0346 0.9665 - 14.000000 1.0571 0.9459 - 15.000000 1.0833 0.9231 - 16.000000 1.1125 0.8989 - 17.000000 1.1441 0.8740 - 18.000000 1.1778 0.8491 - 19.000000 1.2132 0.8243 - 20.000000 1.2500 0.8000 - 21.000000 1.2881 0.7763 - 22.000000 1.3273 0.7534 - 23.000000 1.3674 0.7313 - 24.000000 1.4083 0.7101 - 25.000000 1.4500 0.6897 - 26.000000 1.4923 0.6701 - 27.000000 1.5352 0.6514 - 28.000000 1.5786 0.6335 - 29.000000 1.6224 0.6164 diff --git a/regtest/pycv/rt-jax3/GRADIENT_r.reference b/regtest/pycv/rt-jax3/GRADIENT_r.reference deleted file mode 100644 index 9378690a85..0000000000 --- a/regtest/pycv/rt-jax3/GRADIENT_r.reference +++ /dev/null @@ -1,541 +0,0 @@ -#! FIELDS time parameter r - 0.000000 0 -5.0000 - 0.000000 1 24.7500 - 0.000000 2 0.0000 - 0.000000 3 5.0000 - 0.000000 4 24.7500 - 0.000000 5 0.0000 - 0.000000 6 0.0000 - 0.000000 7 -49.5000 - 0.000000 8 0.0000 - 0.000000 9 -10.0000 - 0.000000 10 0.0000 - 0.000000 11 0.0000 - 0.000000 12 0.0000 - 0.000000 13 4.9500 - 0.000000 14 0.0000 - 0.000000 15 0.0000 - 0.000000 16 0.0000 - 0.000000 17 0.0000 - 1.000000 0 -5.0000 - 1.000000 1 24.7500 - 1.000000 2 0.0000 - 1.000000 3 5.0000 - 1.000000 4 24.7500 - 1.000000 5 0.0000 - 1.000000 6 0.0000 - 1.000000 7 -49.5000 - 1.000000 8 0.0000 - 1.000000 9 -10.0000 - 1.000000 10 0.0000 - 1.000000 11 0.0000 - 1.000000 12 0.0000 - 1.000000 13 4.9500 - 1.000000 14 0.0000 - 1.000000 15 0.0000 - 1.000000 16 0.0000 - 1.000000 17 0.0000 - 2.000000 0 -2.5000 - 2.000000 1 6.0000 - 2.000000 2 0.0000 - 2.000000 3 2.5000 - 2.000000 4 6.0000 - 2.000000 5 0.0000 - 2.000000 6 0.0000 - 2.000000 7 -12.0000 - 2.000000 8 0.0000 - 2.000000 9 -5.0000 - 2.000000 10 0.0000 - 2.000000 11 0.0000 - 2.000000 12 0.0000 - 2.000000 13 2.4000 - 2.000000 14 0.0000 - 2.000000 15 0.0000 - 2.000000 16 0.0000 - 2.000000 17 0.0000 - 3.000000 0 -1.6667 - 3.000000 1 2.5278 - 3.000000 2 0.0000 - 3.000000 3 1.6667 - 3.000000 4 2.5278 - 3.000000 5 0.0000 - 3.000000 6 0.0000 - 3.000000 7 -5.0556 - 3.000000 8 0.0000 - 3.000000 9 -3.3333 - 3.000000 10 0.0000 - 3.000000 11 0.0000 - 3.000000 12 0.0000 - 3.000000 13 1.5167 - 3.000000 14 0.0000 - 3.000000 15 0.0000 - 3.000000 16 0.0000 - 3.000000 17 0.0000 - 4.000000 0 -1.2500 - 4.000000 1 1.3125 - 4.000000 2 0.0000 - 4.000000 3 1.2500 - 4.000000 4 1.3125 - 4.000000 5 0.0000 - 4.000000 6 0.0000 - 4.000000 7 -2.6250 - 4.000000 8 0.0000 - 4.000000 9 -2.5000 - 4.000000 10 0.0000 - 4.000000 11 0.0000 - 4.000000 12 0.0000 - 4.000000 13 1.0500 - 4.000000 14 0.0000 - 4.000000 15 0.0000 - 4.000000 16 0.0000 - 4.000000 17 0.0000 - 5.000000 0 -1.0000 - 5.000000 1 0.7500 - 5.000000 2 0.0000 - 5.000000 3 1.0000 - 5.000000 4 0.7500 - 5.000000 5 0.0000 - 5.000000 6 0.0000 - 5.000000 7 -1.5000 - 5.000000 8 0.0000 - 5.000000 9 -2.0000 - 5.000000 10 0.0000 - 5.000000 11 0.0000 - 5.000000 12 0.0000 - 5.000000 13 0.7500 - 5.000000 14 0.0000 - 5.000000 15 0.0000 - 5.000000 16 0.0000 - 5.000000 17 0.0000 - 6.000000 0 -0.8333 - 6.000000 1 0.4444 - 6.000000 2 0.0000 - 6.000000 3 0.8333 - 6.000000 4 0.4444 - 6.000000 5 0.0000 - 6.000000 6 0.0000 - 6.000000 7 -0.8889 - 6.000000 8 0.0000 - 6.000000 9 -1.6667 - 6.000000 10 0.0000 - 6.000000 11 0.0000 - 6.000000 12 0.0000 - 6.000000 13 0.5333 - 6.000000 14 0.0000 - 6.000000 15 0.0000 - 6.000000 16 0.0000 - 6.000000 17 0.0000 - 7.000000 0 -0.7143 - 7.000000 1 0.2602 - 7.000000 2 0.0000 - 7.000000 3 0.7143 - 7.000000 4 0.2602 - 7.000000 5 0.0000 - 7.000000 6 0.0000 - 7.000000 7 -0.5204 - 7.000000 8 0.0000 - 7.000000 9 -1.4286 - 7.000000 10 0.0000 - 7.000000 11 0.0000 - 7.000000 12 0.0000 - 7.000000 13 0.3643 - 7.000000 14 0.0000 - 7.000000 15 0.0000 - 7.000000 16 0.0000 - 7.000000 17 0.0000 - 8.000000 0 -0.6250 - 8.000000 1 0.1406 - 8.000000 2 0.0000 - 8.000000 3 0.6250 - 8.000000 4 0.1406 - 8.000000 5 0.0000 - 8.000000 6 0.0000 - 8.000000 7 -0.2812 - 8.000000 8 0.0000 - 8.000000 9 -1.2500 - 8.000000 10 0.0000 - 8.000000 11 0.0000 - 8.000000 12 0.0000 - 8.000000 13 0.2250 - 8.000000 14 0.0000 - 8.000000 15 0.0000 - 8.000000 16 0.0000 - 8.000000 17 0.0000 - 9.000000 0 -0.5556 - 9.000000 1 0.0586 - 9.000000 2 0.0000 - 9.000000 3 0.5556 - 9.000000 4 0.0586 - 9.000000 5 0.0000 - 9.000000 6 0.0000 - 9.000000 7 -0.1173 - 9.000000 8 0.0000 - 9.000000 9 -1.1111 - 9.000000 10 0.0000 - 9.000000 11 0.0000 - 9.000000 12 0.0000 - 9.000000 13 0.1056 - 9.000000 14 0.0000 - 9.000000 15 0.0000 - 9.000000 16 0.0000 - 9.000000 17 0.0000 - 10.000000 0 -0.5000 - 10.000000 1 0.0000 - 10.000000 2 0.0000 - 10.000000 3 0.5000 - 10.000000 4 0.0000 - 10.000000 5 0.0000 - 10.000000 6 0.0000 - 10.000000 7 0.0000 - 10.000000 8 0.0000 - 10.000000 9 -1.0000 - 10.000000 10 0.0000 - 10.000000 11 0.0000 - 10.000000 12 0.0000 - 10.000000 13 0.0000 - 10.000000 14 0.0000 - 10.000000 15 0.0000 - 10.000000 16 0.0000 - 10.000000 17 0.0000 - 11.000000 0 -0.4545 - 11.000000 1 -0.0434 - 11.000000 2 0.0000 - 11.000000 3 0.4545 - 11.000000 4 -0.0434 - 11.000000 5 0.0000 - 11.000000 6 0.0000 - 11.000000 7 0.0868 - 11.000000 8 0.0000 - 11.000000 9 -0.9091 - 11.000000 10 0.0000 - 11.000000 11 0.0000 - 11.000000 12 0.0000 - 11.000000 13 -0.0955 - 11.000000 14 0.0000 - 11.000000 15 0.0000 - 11.000000 16 0.0000 - 11.000000 17 0.0000 - 12.000000 0 -0.4167 - 12.000000 1 -0.0764 - 12.000000 2 0.0000 - 12.000000 3 0.4167 - 12.000000 4 -0.0764 - 12.000000 5 0.0000 - 12.000000 6 0.0000 - 12.000000 7 0.1528 - 12.000000 8 0.0000 - 12.000000 9 -0.8333 - 12.000000 10 0.0000 - 12.000000 11 0.0000 - 12.000000 12 0.0000 - 12.000000 13 -0.1833 - 12.000000 14 0.0000 - 12.000000 15 0.0000 - 12.000000 16 0.0000 - 12.000000 17 0.0000 - 13.000000 0 -0.3846 - 13.000000 1 -0.1021 - 13.000000 2 0.0000 - 13.000000 3 0.3846 - 13.000000 4 -0.1021 - 13.000000 5 0.0000 - 13.000000 6 0.0000 - 13.000000 7 0.2041 - 13.000000 8 0.0000 - 13.000000 9 -0.7692 - 13.000000 10 0.0000 - 13.000000 11 0.0000 - 13.000000 12 0.0000 - 13.000000 13 -0.2654 - 13.000000 14 0.0000 - 13.000000 15 0.0000 - 13.000000 16 0.0000 - 13.000000 17 0.0000 - 14.000000 0 -0.3571 - 14.000000 1 -0.1224 - 14.000000 2 0.0000 - 14.000000 3 0.3571 - 14.000000 4 -0.1224 - 14.000000 5 0.0000 - 14.000000 6 0.0000 - 14.000000 7 0.2449 - 14.000000 8 0.0000 - 14.000000 9 -0.7143 - 14.000000 10 0.0000 - 14.000000 11 0.0000 - 14.000000 12 0.0000 - 14.000000 13 -0.3429 - 14.000000 14 0.0000 - 14.000000 15 0.0000 - 14.000000 16 0.0000 - 14.000000 17 0.0000 - 15.000000 0 -0.3333 - 15.000000 1 -0.1389 - 15.000000 2 0.0000 - 15.000000 3 0.3333 - 15.000000 4 -0.1389 - 15.000000 5 0.0000 - 15.000000 6 0.0000 - 15.000000 7 0.2778 - 15.000000 8 0.0000 - 15.000000 9 -0.6667 - 15.000000 10 0.0000 - 15.000000 11 0.0000 - 15.000000 12 0.0000 - 15.000000 13 -0.4167 - 15.000000 14 0.0000 - 15.000000 15 0.0000 - 15.000000 16 0.0000 - 15.000000 17 0.0000 - 16.000000 0 -0.3125 - 16.000000 1 -0.1523 - 16.000000 2 0.0000 - 16.000000 3 0.3125 - 16.000000 4 -0.1523 - 16.000000 5 0.0000 - 16.000000 6 0.0000 - 16.000000 7 0.3047 - 16.000000 8 0.0000 - 16.000000 9 -0.6250 - 16.000000 10 0.0000 - 16.000000 11 0.0000 - 16.000000 12 0.0000 - 16.000000 13 -0.4875 - 16.000000 14 0.0000 - 16.000000 15 0.0000 - 16.000000 16 0.0000 - 16.000000 17 0.0000 - 17.000000 0 -0.2941 - 17.000000 1 -0.1635 - 17.000000 2 0.0000 - 17.000000 3 0.2941 - 17.000000 4 -0.1635 - 17.000000 5 0.0000 - 17.000000 6 0.0000 - 17.000000 7 0.3270 - 17.000000 8 0.0000 - 17.000000 9 -0.5882 - 17.000000 10 0.0000 - 17.000000 11 0.0000 - 17.000000 12 0.0000 - 17.000000 13 -0.5559 - 17.000000 14 0.0000 - 17.000000 15 0.0000 - 17.000000 16 0.0000 - 17.000000 17 0.0000 - 18.000000 0 -0.2778 - 18.000000 1 -0.1728 - 18.000000 2 0.0000 - 18.000000 3 0.2778 - 18.000000 4 -0.1728 - 18.000000 5 0.0000 - 18.000000 6 0.0000 - 18.000000 7 0.3457 - 18.000000 8 0.0000 - 18.000000 9 -0.5556 - 18.000000 10 0.0000 - 18.000000 11 0.0000 - 18.000000 12 0.0000 - 18.000000 13 -0.6222 - 18.000000 14 0.0000 - 18.000000 15 0.0000 - 18.000000 16 0.0000 - 18.000000 17 0.0000 - 19.000000 0 -0.2632 - 19.000000 1 -0.1807 - 19.000000 2 0.0000 - 19.000000 3 0.2632 - 19.000000 4 -0.1807 - 19.000000 5 0.0000 - 19.000000 6 0.0000 - 19.000000 7 0.3615 - 19.000000 8 0.0000 - 19.000000 9 -0.5263 - 19.000000 10 0.0000 - 19.000000 11 0.0000 - 19.000000 12 0.0000 - 19.000000 13 -0.6868 - 19.000000 14 0.0000 - 19.000000 15 0.0000 - 19.000000 16 0.0000 - 19.000000 17 0.0000 - 20.000000 0 -0.2500 - 20.000000 1 -0.1875 - 20.000000 2 0.0000 - 20.000000 3 0.2500 - 20.000000 4 -0.1875 - 20.000000 5 0.0000 - 20.000000 6 0.0000 - 20.000000 7 0.3750 - 20.000000 8 0.0000 - 20.000000 9 -0.5000 - 20.000000 10 0.0000 - 20.000000 11 0.0000 - 20.000000 12 0.0000 - 20.000000 13 -0.7500 - 20.000000 14 0.0000 - 20.000000 15 0.0000 - 20.000000 16 0.0000 - 20.000000 17 0.0000 - 21.000000 0 -0.2381 - 21.000000 1 -0.1933 - 21.000000 2 0.0000 - 21.000000 3 0.2381 - 21.000000 4 -0.1933 - 21.000000 5 0.0000 - 21.000000 6 0.0000 - 21.000000 7 0.3866 - 21.000000 8 0.0000 - 21.000000 9 -0.4762 - 21.000000 10 0.0000 - 21.000000 11 0.0000 - 21.000000 12 0.0000 - 21.000000 13 -0.8119 - 21.000000 14 0.0000 - 21.000000 15 0.0000 - 21.000000 16 0.0000 - 21.000000 17 0.0000 - 22.000000 0 -0.2273 - 22.000000 1 -0.1983 - 22.000000 2 0.0000 - 22.000000 3 0.2273 - 22.000000 4 -0.1983 - 22.000000 5 0.0000 - 22.000000 6 0.0000 - 22.000000 7 0.3967 - 22.000000 8 0.0000 - 22.000000 9 -0.4545 - 22.000000 10 0.0000 - 22.000000 11 0.0000 - 22.000000 12 0.0000 - 22.000000 13 -0.8727 - 22.000000 14 0.0000 - 22.000000 15 0.0000 - 22.000000 16 0.0000 - 22.000000 17 0.0000 - 23.000000 0 -0.2174 - 23.000000 1 -0.2027 - 23.000000 2 0.0000 - 23.000000 3 0.2174 - 23.000000 4 -0.2027 - 23.000000 5 0.0000 - 23.000000 6 0.0000 - 23.000000 7 0.4055 - 23.000000 8 0.0000 - 23.000000 9 -0.4348 - 23.000000 10 0.0000 - 23.000000 11 0.0000 - 23.000000 12 0.0000 - 23.000000 13 -0.9326 - 23.000000 14 0.0000 - 23.000000 15 0.0000 - 23.000000 16 0.0000 - 23.000000 17 0.0000 - 24.000000 0 -0.2083 - 24.000000 1 -0.2066 - 24.000000 2 0.0000 - 24.000000 3 0.2083 - 24.000000 4 -0.2066 - 24.000000 5 0.0000 - 24.000000 6 0.0000 - 24.000000 7 0.4132 - 24.000000 8 0.0000 - 24.000000 9 -0.4167 - 24.000000 10 0.0000 - 24.000000 11 0.0000 - 24.000000 12 0.0000 - 24.000000 13 -0.9917 - 24.000000 14 0.0000 - 24.000000 15 0.0000 - 24.000000 16 0.0000 - 24.000000 17 0.0000 - 25.000000 0 -0.2000 - 25.000000 1 -0.2100 - 25.000000 2 0.0000 - 25.000000 3 0.2000 - 25.000000 4 -0.2100 - 25.000000 5 0.0000 - 25.000000 6 0.0000 - 25.000000 7 0.4200 - 25.000000 8 0.0000 - 25.000000 9 -0.4000 - 25.000000 10 0.0000 - 25.000000 11 0.0000 - 25.000000 12 0.0000 - 25.000000 13 -1.0500 - 25.000000 14 0.0000 - 25.000000 15 0.0000 - 25.000000 16 0.0000 - 25.000000 17 0.0000 - 26.000000 0 -0.1923 - 26.000000 1 -0.2130 - 26.000000 2 0.0000 - 26.000000 3 0.1923 - 26.000000 4 -0.2130 - 26.000000 5 0.0000 - 26.000000 6 0.0000 - 26.000000 7 0.4260 - 26.000000 8 0.0000 - 26.000000 9 -0.3846 - 26.000000 10 0.0000 - 26.000000 11 0.0000 - 26.000000 12 0.0000 - 26.000000 13 -1.1077 - 26.000000 14 0.0000 - 26.000000 15 0.0000 - 26.000000 16 0.0000 - 26.000000 17 0.0000 - 27.000000 0 -0.1852 - 27.000000 1 -0.2157 - 27.000000 2 0.0000 - 27.000000 3 0.1852 - 27.000000 4 -0.2157 - 27.000000 5 0.0000 - 27.000000 6 0.0000 - 27.000000 7 0.4314 - 27.000000 8 0.0000 - 27.000000 9 -0.3704 - 27.000000 10 0.0000 - 27.000000 11 0.0000 - 27.000000 12 0.0000 - 27.000000 13 -1.1648 - 27.000000 14 0.0000 - 27.000000 15 0.0000 - 27.000000 16 0.0000 - 27.000000 17 0.0000 - 28.000000 0 -0.1786 - 28.000000 1 -0.2181 - 28.000000 2 0.0000 - 28.000000 3 0.1786 - 28.000000 4 -0.2181 - 28.000000 5 0.0000 - 28.000000 6 0.0000 - 28.000000 7 0.4362 - 28.000000 8 0.0000 - 28.000000 9 -0.3571 - 28.000000 10 0.0000 - 28.000000 11 0.0000 - 28.000000 12 0.0000 - 28.000000 13 -1.2214 - 28.000000 14 0.0000 - 28.000000 15 0.0000 - 28.000000 16 0.0000 - 28.000000 17 0.0000 - 29.000000 0 -0.1724 - 29.000000 1 -0.2203 - 29.000000 2 0.0000 - 29.000000 3 0.1724 - 29.000000 4 -0.2203 - 29.000000 5 0.0000 - 29.000000 6 0.0000 - 29.000000 7 0.4405 - 29.000000 8 0.0000 - 29.000000 9 -0.3448 - 29.000000 10 0.0000 - 29.000000 11 0.0000 - 29.000000 12 0.0000 - 29.000000 13 -1.2776 - 29.000000 14 0.0000 - 29.000000 15 0.0000 - 29.000000 16 0.0000 - 29.000000 17 0.0000 diff --git a/regtest/pycv/rt-jax3/Makefile b/regtest/pycv/rt-jax3/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-jax3/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-jax3/arc3.xyz b/regtest/pycv/rt-jax3/arc3.xyz deleted file mode 100644 index 2d4c50d84d..0000000000 --- a/regtest/pycv/rt-jax3/arc3.xyz +++ /dev/null @@ -1,150 +0,0 @@ -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.100000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.100000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.200000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.300000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.400000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.500000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.600000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.700000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.800000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 0.900000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.000000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.100000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.200000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.300000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.400000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.500000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.600000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.700000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.800000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 1.900000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.000000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.100000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.200000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.300000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.400000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.500000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.600000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.700000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.800000 0 -3 -10 0 0 0 10 0 0 0 10 -X -1 0 0 -X 1 0 0 -X 0 2.900000 0 diff --git a/regtest/pycv/rt-jax3/config b/regtest/pycv/rt-jax3/config deleted file mode 100644 index 14a4e9566a..0000000000 --- a/regtest/pycv/rt-jax3/config +++ /dev/null @@ -1,7 +0,0 @@ -# This is the same example of three atoms on an arc checked with the -# symbolic calculations notebook. - -type=driver -arg="--plumed plumed.dat --ixyz arc3.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -PLUMED_ALLOW_SKIP_ON_TRAVIS=yes -plumed_modules=pycv diff --git a/regtest/pycv/rt-jax3/curvature.py b/regtest/pycv/rt-jax3/curvature.py deleted file mode 100644 index 6e14c2cc6a..0000000000 --- a/regtest/pycv/rt-jax3/curvature.py +++ /dev/null @@ -1,36 +0,0 @@ -# Same calculation (and results) w.r.t. https://doi.org/10.1016/j.cpc.2018.02.017 -# -# (first frame returning NANs was removed) -# https://github.com/tonigi/plumed2-automatic-gradients/tree/automatic-gradient-computation/regtest/curvature_codegen - - -# Import the JAX library -import jax.numpy as np -from jax import grad, jit - -# Implementation of the angle function. @jit really improves speed -@jit -def r_f(x): - r21 = x[0,:]-x[1,:] - r23 = x[2,:]-x[1,:] - r13 = x[2,:]-x[0,:] - - cos2theta = np.dot(r21,r23)**2 / (np.dot(r21,r21) * np.dot(r23,r23)) - sin2theta = 1-cos2theta - - R2= np.dot(r13,r13)/sin2theta/4.0 - return np.sqrt(R2) - -# Use JAX to auto-gradient it -r_g = grad(r_f) - -# The CV function actually called -def r(x): - return r_f(x), r_g(x) - - -# Differentiation is trivial here -@jit -def inv(x): - return 1/x, -(x**-2) - diff --git a/regtest/pycv/rt-jax3/plumed.dat b/regtest/pycv/rt-jax3/plumed.dat deleted file mode 100644 index 3787e377fd..0000000000 --- a/regtest/pycv/rt-jax3/plumed.dat +++ /dev/null @@ -1,12 +0,0 @@ - -r: PYTHONCV ATOMS=1,2,3 IMPORT=curvature FUNCTION=r -ir: PYTHONFUNCTION ARG=r IMPORT=curvature FUNCTION=inv PERIODIC=NO - - -DUMPDERIVATIVES ARG=r FILE=GRADIENT_r FMT=%8.4f -# DUMPDERIVATIVES ARG=ir FILE=GRADIENT_ir FMT=%8.4f - -PRINT FILE=COLVAR ARG=* FMT=%8.4f - - - diff --git a/regtest/pycv/rt-multi-1/Makefile b/regtest/pycv/rt-multi-1/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-multi-1/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-multi-1/colvar.out.reference b/regtest/pycv/rt-multi-1/colvar.out.reference deleted file mode 100644 index fcd27d03ea..0000000000 --- a/regtest/pycv/rt-multi-1/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1.py-d12 cv1.py-d13 cv12a cv13a - 0.000000 7.071068 5.000000 7.071068 5.000000 - 1.000000 7.071068 8.660254 7.071068 8.660254 - 2.000000 7.071068 11.180340 7.071068 11.180340 - 3.000000 7.071068 8.660254 7.071068 8.660254 diff --git a/regtest/pycv/rt-multi-1/config b/regtest/pycv/rt-multi-1/config deleted file mode 100644 index 6839ec1758..0000000000 --- a/regtest/pycv/rt-multi-1/config +++ /dev/null @@ -1,4 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -plumed_modules=pycv diff --git a/regtest/pycv/rt-multi-1/distcv.py b/regtest/pycv/rt-multi-1/distcv.py deleted file mode 100644 index 40c74491a5..0000000000 --- a/regtest/pycv/rt-multi-1/distcv.py +++ /dev/null @@ -1,45 +0,0 @@ -import numpy as np - -# In reality one should not log stuff here... -log=open("log.txt","w",1) - -print("At import",file=log) - - -# Define the distance function -def dist(x): - r = x[0,:]-x[1,:] - d2 = np.dot(r,r) - return np.sqrt(d2) - -def grad_dist(x): - d = dist(x) - r = x[0,:]-x[1,:] - g = r/d - return np.array([g,-g]) - - -# The CV function actually called -def cv(X): - print("At CV",file=log) - row12 = np.array([0,1]) - row13 = np.array([0,2]) - - X12 = X[row12,:] - X13 = X[row13,:] - - rf = { - 'd12': dist(X12), - 'd13': dist(X13) - } - - gd12 = grad_dist(X12) - gd13 = grad_dist(X13) - - rg = { - 'd12': np.array([ gd12[0,:], gd12[1,:], [0.,0.,0.] ]), - 'd13': np.array([ gd13[0,:], [0.,0.,0.], gd13[1,:] ]) - } - - return rf, rg - diff --git a/regtest/pycv/rt-multi-1/plumed.dat b/regtest/pycv/rt-multi-1/plumed.dat deleted file mode 100644 index c77950b1ac..0000000000 --- a/regtest/pycv/rt-multi-1/plumed.dat +++ /dev/null @@ -1,14 +0,0 @@ - -cv1: PYTHONCV ATOMS=1,3,4 IMPORT=distcv FUNCTION=cv COMPONENTS=d12,d13 - -cv12a: DISTANCE ATOMS=1,3 -cv13a: DISTANCE ATOMS=1,4 - -DUMPDERIVATIVES ARG=cv1.py-d12 FILE=GRAD_cv1d12 FMT=%.4f -DUMPDERIVATIVES ARG=cv1.py-d13 FILE=GRAD_cv1d13 FMT=%.4f -DUMPDERIVATIVES ARG=cv12a FILE=GRAD_cv12a FMT=%.4f -DUMPDERIVATIVES ARG=cv13a FILE=GRAD_cv13a FMT=%.4f - -# RESTRAINT AT=0 SLOPE=-1 ARG=cv1 - -PRINT FILE=colvar.out ARG=* diff --git a/regtest/pycv/rt-multi-1/traj.xyz b/regtest/pycv/rt-multi-1/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-multi-1/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-multi-2-jax/Makefile b/regtest/pycv/rt-multi-2-jax/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-multi-2-jax/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-multi-2-jax/colvar.out.reference b/regtest/pycv/rt-multi-2-jax/colvar.out.reference deleted file mode 100644 index fcd27d03ea..0000000000 --- a/regtest/pycv/rt-multi-2-jax/colvar.out.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time cv1.py-d12 cv1.py-d13 cv12a cv13a - 0.000000 7.071068 5.000000 7.071068 5.000000 - 1.000000 7.071068 8.660254 7.071068 8.660254 - 2.000000 7.071068 11.180340 7.071068 11.180340 - 3.000000 7.071068 8.660254 7.071068 8.660254 diff --git a/regtest/pycv/rt-multi-2-jax/config b/regtest/pycv/rt-multi-2-jax/config deleted file mode 100644 index a7cc659930..0000000000 --- a/regtest/pycv/rt-multi-2-jax/config +++ /dev/null @@ -1,5 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -PLUMED_ALLOW_SKIP_ON_TRAVIS=yes -plumed_modules=pycv diff --git a/regtest/pycv/rt-multi-2-jax/distcv.py b/regtest/pycv/rt-multi-2-jax/distcv.py deleted file mode 100644 index 4151dba4c3..0000000000 --- a/regtest/pycv/rt-multi-2-jax/distcv.py +++ /dev/null @@ -1,19 +0,0 @@ -import jax.numpy as np -from jax import jacrev, jit - - -# Define the distance function -@jit -def cv_f(X): - return { - 'd12': np.linalg.norm( X[0,:]-X[1,:] ), - 'd13': np.linalg.norm( X[0,:]-X[2,:] ) - } - -cv_j=jacrev(cv_f) - - -# The CV function actually called -def cv(X): - return cv_f(X), cv_j(X) - diff --git a/regtest/pycv/rt-multi-2-jax/plumed.dat b/regtest/pycv/rt-multi-2-jax/plumed.dat deleted file mode 100644 index fdc90940fa..0000000000 --- a/regtest/pycv/rt-multi-2-jax/plumed.dat +++ /dev/null @@ -1,17 +0,0 @@ - -cv1: PYTHONCV ATOMS=1,3,4 IMPORT=distcv FUNCTION=cv COMPONENTS=d12,d13 - -cv12a: DISTANCE ATOMS=1,3 -cv13a: DISTANCE ATOMS=1,4 - -DUMPDERIVATIVES ARG=cv1.py-d12 FILE=GRAD_cv1d12 FMT=%.4f -DUMPDERIVATIVES ARG=cv1.py-d13 FILE=GRAD_cv1d13 FMT=%.4f -DUMPDERIVATIVES ARG=cv12a FILE=GRAD_cv12a FMT=%.4f -DUMPDERIVATIVES ARG=cv13a FILE=GRAD_cv13a FMT=%.4f - -# RESTRAINT AT=0 SLOPE=-1 ARG=cv1 - -PRINT FILE=colvar.out ARG=* - - - diff --git a/regtest/pycv/rt-multi-2-jax/traj.xyz b/regtest/pycv/rt-multi-2-jax/traj.xyz deleted file mode 100644 index c0e66cf2b2..0000000000 --- a/regtest/pycv/rt-multi-2-jax/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 5 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X -5 5 0 -4 -100 100 100 -X 5 0 0 -X 0 0 0 -X 0 5 0 -X 0 5 -5 diff --git a/regtest/pycv/rt-pbc/Makefile b/regtest/pycv/rt-pbc/Makefile deleted file mode 100644 index 3703b27cea..0000000000 --- a/regtest/pycv/rt-pbc/Makefile +++ /dev/null @@ -1 +0,0 @@ -include ../../scripts/test.make diff --git a/regtest/pycv/rt-pbc/colvar.reference b/regtest/pycv/rt-pbc/colvar.reference deleted file mode 100644 index ede02e056e..0000000000 --- a/regtest/pycv/rt-pbc/colvar.reference +++ /dev/null @@ -1,5 +0,0 @@ -#! FIELDS time diff diffnpbc - 0.000000 -0.0000 0.0000 - 1.000000 -0.0000 0.0000 - 2.000000 0.0000 -0.0000 - 3.000000 -0.0000 -0.0000 diff --git a/regtest/pycv/rt-pbc/config b/regtest/pycv/rt-pbc/config deleted file mode 100644 index 6839ec1758..0000000000 --- a/regtest/pycv/rt-pbc/config +++ /dev/null @@ -1,4 +0,0 @@ - -type=driver -arg="--plumed plumed.dat --ixyz traj.xyz --dump-forces forces --dump-forces-fmt=%10.6f" -plumed_modules=pycv diff --git a/regtest/pycv/rt-pbc/forces.reference b/regtest/pycv/rt-pbc/forces.reference deleted file mode 100644 index 2d2bbe7469..0000000000 --- a/regtest/pycv/rt-pbc/forces.reference +++ /dev/null @@ -1,24 +0,0 @@ -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -4 - 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 -X 0.000000 0.000000 0.000000 diff --git a/regtest/pycv/rt-pbc/plumed.dat b/regtest/pycv/rt-pbc/plumed.dat deleted file mode 100644 index ac425e3a09..0000000000 --- a/regtest/pycv/rt-pbc/plumed.dat +++ /dev/null @@ -1,15 +0,0 @@ -# LOAD FILE=PythonCV.dylib - -pycvnpbc: PYTHONCV ATOMS=1,4 IMPORT=pycv FUNCTION=cv1 NOPBC - -cvnpbc: DISTANCE ATOMS=1,4 NOPBC - -pycv: PYTHONCV ATOMS=1,4 IMPORT=pycv FUNCTION=cv1 - -cv: DISTANCE ATOMS=1,4 - -diffnpbc: CUSTOM ARG=cvnpbc,pycvnpbc FUNC=y-x PERIODIC=NO -diff: CUSTOM ARG=cv,pycv FUNC=y-x PERIODIC=NO - -PRINT ARG=diff,diffnpbc FILE=colvar FMT=%8.4f STRIDE=1 -PRINT ARG=pycv,cv,pycvnpbc,cvnpbc FILE=colvar.out FMT=%8.4f STRIDE=1 diff --git a/regtest/pycv/rt-pbc/pycv.py b/regtest/pycv/rt-pbc/pycv.py deleted file mode 100644 index 5bb95959ea..0000000000 --- a/regtest/pycv/rt-pbc/pycv.py +++ /dev/null @@ -1,18 +0,0 @@ -# This is only a partial example. This function does not compute the -# gradient, so it is useless for biasing. See the other regression -# tests for how to auto-grad. - -# And, of course, one should not call slow functions (such as print) -# in the CV calculation. - -import numpy as np -log=open("pycv.log","w") - -print("Imported.",file=log) - -def cv1(x): - print(x,file=log) # But don't - d = x[0,:]-x[1,:] - d2 = np.dot(d,d) - # If computing a gradient, return it as a 2nd return value. - return np.sqrt(d2) diff --git a/regtest/pycv/rt-pbc/traj.xyz b/regtest/pycv/rt-pbc/traj.xyz deleted file mode 100644 index 19f0e8b070..0000000000 --- a/regtest/pycv/rt-pbc/traj.xyz +++ /dev/null @@ -1,24 +0,0 @@ -4 -10 10 10 -X 0 0 0 -X 0 0 0 -X 0 0 0 -X 0 8 0 -4 -10 10 10 -X 0 0 0 -X 0 0 0 -X 0 0 0 -X 0 -2 0 -4 -10 10 10 -X 0 0 0 -X 0 0 0 -X 0 0 0 -X 0 5 10 -4 -10 10 10 -X 0 0 0 -X 0 0 0 -X 0 0 0 -X 1 1 1