start reworking Python API

- add interface class wrapping the CDLL - sanity check for ndarrays (type, size) - rework ASE Calculator to be independent of the ctypes interface - add unit test for the three Hamiltonians - add mypy, pytest and pylint to meson.build - ignore __pycache__ in the working directory - moved old xtb.py to scripts - flake8 test in meson.build - additional test for the library interface - added GBSA Python API - GFN1 return now charges, dipole moments and bond orders - unified interface for molecular and periodic GFN0 - updated setup.py and corresponding README - allows passing number of unpaired electrons to the API - fix test with unpaired electrons - added stress tensor as property to GFN0 Calculator - updated description for Python package - added a sanity check for multiplicities and electron number - adjusted optimization script for new setup
grimme-lab · Oct 9, 2019 · aa9f2e2 · aa9f2e2
1 parent b991002
commit aa9f2e2
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Showing 25 changed files with 2,272 additions and 897 deletions.
diff --git a/.gitignore b/.gitignore
@@ -59,3 +59,9 @@ xtbopt.xyz
 xtbopt.sdf
 xtbopt.coord
 xtbopt.log
+
+# python build artefacts
+__pycache__/
+python/dist
+python/build
+*.egg-info
diff --git a/TESTSUITE/cpp_api_example.cpp b/TESTSUITE/cpp_api_example.cpp
@@ -22,15 +22,15 @@ main (int argc, char **argv)
        1.92825631079613, 0.00000000000000,-2.53624948351102,
        0.00000000000000, 0.00000000000000, 5.23010455462158};
 
-   const xtb::SCC_options opt {2, 0, 1.0, 300.0, true, false, 30, "none"};
+   const xtb::SCC_options opt {2, 0, 1.0, 300.0, true, false, true, 30, "none"};
 
    double energy {0.0};
    double dipole[3] {0.0};
    double q[natoms] {0.0};
    double qp[6*natoms] {0.0};
    double wbo[natoms*natoms] {0.0};
 
-   int stat = xtb::GFN2_calculation(&natoms, attyp, &charge, coord, &opt, "-",
+   int stat = xtb::GFN2_calculation(&natoms, attyp, &charge, nullptr, coord, &opt, "-",
                                     &energy, nullptr, dipole, q, nullptr, qp, wbo);
 
    assert(stat == 0);

diff --git a/TESTSUITE/gfn0.f90 b/TESTSUITE/gfn0.f90
@@ -64,7 +64,7 @@ subroutine test_gfn0_sp
    mol%xyz = xyz
    mol%chrg = 0.0_wp
    call mol%set_nuclear_charge
-   call mol%calculate_distances
+   call mol%update
 
    wfn%nel = idint(sum(mol%z))
    wfn%nopen = 0
@@ -160,7 +160,7 @@ subroutine test_gfn0_api
 
    real(wp) :: energy
    real(wp) :: hl_gap
-   real(wp) :: gradlatt(3,3)
+   real(wp) :: dum(3,3)
    real(wp),allocatable :: gradient(:,:)
 
    ! setup the environment variables
@@ -169,14 +169,15 @@ subroutine test_gfn0_api
    call mol%allocate(nat)
    mol%at   = at
    mol%xyz  = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
    gradient = 0.0_wp
 
    call gfn0_calculation &
-      (istdout,env,opt,mol,gfn,hl_gap,energy,gradient)
+      (istdout,env,opt,mol,gfn,hl_gap,energy,gradient,dum,dum)
 
    call assert_close(hl_gap, 5.5384029314207_wp,thr)
    call assert_close(energy,-8.6908532561691_wp,thr)

diff --git a/TESTSUITE/gfn1.f90 b/TESTSUITE/gfn1.f90
@@ -54,12 +54,13 @@ subroutine test_gfn1_scc
    mol%xyz = xyz
    mol%chrg = 0.0_wp
    call mol%set_nuclear_charge
+   call mol%update
 
    wfn%nel = idint(sum(mol%z))
    wfn%nopen = 0
 
    allocate( g(3,mol%n), source = 0.0_wp )
- 
+
    call use_parameterset('.param_gfn.xtb',globpar,okpar)
    call assert(okpar)
 
@@ -124,6 +125,7 @@ subroutine test_gfn1_api
    use tbdef_molecule
    use tbdef_param
    use tbdef_pcem
+   use tbdef_wavefunction
 
    use tb_calculators
 
@@ -147,6 +149,7 @@ subroutine test_gfn1_api
    type(tb_environment) :: env
    type(gfn_parameter)  :: gfn
    type(tb_pcem)        :: pcem
+   type(tb_wavefunction):: wfn
 
    real(wp) :: energy
    real(wp) :: hl_gap
@@ -158,14 +161,15 @@ subroutine test_gfn1_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
    gradient = 0.0_wp
 
    call gfn1_calculation &
-      (istdout,env,opt,mol,gfn,pcem,hl_gap,energy,gradient)
+      (istdout,env,opt,mol,gfn,pcem,wfn,hl_gap,energy,gradient)
 
    call assert_close(hl_gap, 5.6067613075402_wp,thr)
    call assert_close(energy,-8.4156335932985_wp,thr)
@@ -189,6 +193,7 @@ subroutine test_gfn1gbsa_api
    use tbdef_molecule
    use tbdef_param
    use tbdef_pcem
+   use tbdef_wavefunction
 
    use tb_calculators
 
@@ -214,6 +219,7 @@ subroutine test_gfn1gbsa_api
    type(tb_environment) :: env
    type(gfn_parameter)  :: gfn
    type(tb_pcem)        :: pcem
+   type(tb_wavefunction):: wfn
 
    real(wp) :: energy
    real(wp) :: hl_gap
@@ -225,14 +231,15 @@ subroutine test_gfn1gbsa_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
    gradient = 0.0_wp
 
    call gfn1_calculation &
-      (istdout,env,opt,mol,gfn,pcem,hl_gap,energy,gradient)
+      (istdout,env,opt,mol,gfn,pcem,wfn,hl_gap,energy,gradient)
 
    call assert_close(hl_gap, 6.641641300724_wp,1e-4_wp)
    call assert_close(energy,-14.215790820910_wp,thr)
@@ -255,6 +262,7 @@ subroutine test_gfn1_pcem_api
    use tbdef_molecule
    use tbdef_param
    use tbdef_pcem
+   use tbdef_wavefunction
 
    use aoparam
 
@@ -288,6 +296,7 @@ subroutine test_gfn1_pcem_api
    type(tb_environment) :: env
    type(gfn_parameter)  :: gfn
    type(tb_pcem)        :: pcem
+   type(tb_wavefunction):: wfn
 
    real(wp) :: energy
    real(wp) :: hl_gap
@@ -299,14 +308,15 @@ subroutine test_gfn1_pcem_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
    gradient = 0.0_wp
 
    call gfn1_calculation &
-      (istdout,env,opt,mol,gfn,pcem,hl_gap,energy,gradient)
+      (istdout,env,opt,mol,gfn,pcem,wfn,hl_gap,energy,gradient)
 
    call assert_close(hl_gap, 9.0155275960407_wp,thr*10)
    call assert_close(energy,-23.113490916186_wp,thr)
@@ -325,7 +335,8 @@ subroutine test_gfn1_pcem_api
    call mol%allocate(nat2)
    mol%at  = at(:nat2)
    mol%xyz = xyz(:,:nat2)
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    call pcem%allocate(nat2)
    pcem%xyz = xyz(:,nat2+1:)
@@ -335,7 +346,7 @@ subroutine test_gfn1_pcem_api
    pcem%grd = 0.0_wp
 
    call gfn1_calculation &
-      (istdout,env,opt,mol,gfn,pcem,hl_gap,energy,gradient)
+      (istdout,env,opt,mol,gfn,pcem,wfn,hl_gap,energy,gradient)
 
    call assert_close(hl_gap, 8.7253450666347_wp,thr)
    call assert_close(energy,-11.559896105984_wp,thr)
@@ -359,7 +370,7 @@ subroutine test_gfn1_pcem_api
    pcem%gam = 999.0_wp ! point charges
 
    call gfn1_calculation &
-      (istdout,env,opt,mol,gfn,pcem,hl_gap,energy,gradient)
+      (istdout,env,opt,mol,gfn,pcem,wfn,hl_gap,energy,gradient)
 
    call assert_close(hl_gap, 8.9183046297437_wp,thr)
    call assert_close(energy,-11.565012263827_wp,thr)

diff --git a/TESTSUITE/gfn2.f90 b/TESTSUITE/gfn2.f90
@@ -54,6 +54,7 @@ subroutine test_gfn2_scc
    mol%xyz = xyz
    mol%chrg = 0.0_wp
    call mol%set_nuclear_charge
+   call mol%update
 
    wfn%nel = idint(sum(mol%z))
    wfn%nopen = 0
@@ -167,7 +168,8 @@ subroutine test_gfn2_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
@@ -239,7 +241,8 @@ subroutine test_gfn2gbsa_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
@@ -309,7 +312,8 @@ subroutine test_gfn2salt_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
@@ -390,7 +394,8 @@ subroutine test_gfn2_pcem_api
    call mol%allocate(nat)
    mol%at  = at
    mol%xyz = xyz
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
@@ -416,7 +421,8 @@ subroutine test_gfn2_pcem_api
    call mol%allocate(nat2)
    mol%at  = at(:nat2)
    mol%xyz = xyz(:,:nat2)
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    call pcem%allocate(nat2)
    pcem%xyz = xyz(:,nat2+1:)

diff --git a/TESTSUITE/peeq.f90 b/TESTSUITE/peeq.f90
@@ -202,6 +202,7 @@ subroutine test_peeq_api
    real(wp) :: energy
    real(wp) :: hl_gap
    real(wp) :: gradlatt(3,3)
+   real(wp) :: stress(3,3)
    real(wp),allocatable :: gradient(:,:)
 
    ! setup the environment variables
@@ -217,7 +218,8 @@ subroutine test_peeq_api
    call dlat_to_cell(lattice,mol%cellpar)
    call dlat_to_rlat(lattice,mol%rec_lat)
    call coord_trafo(nat,lattice,abc,mol%xyz)
-   call mol%calculate_distances
+   call mol%set_nuclear_charge
+   call mol%update
 
    allocate(gradient(3,mol%n))
    energy = 0.0_wp
@@ -226,8 +228,8 @@ subroutine test_peeq_api
 
    call mctc_mute
 
-   call peeq_calculation &
-      (istdout,env,opt,mol,gfn,hl_gap,energy,gradient,gradlatt)
+   call gfn0_calculation &
+      (istdout,env,opt,mol,gfn,hl_gap,energy,gradient,stress,gradlatt)
 
    call assert_close(hl_gap, 4.8620892163953_wp,thr)
    call assert_close(energy,-8.4930019025474_wp,thr)