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Remove dead code from the TPR parser #3516

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Feb 3, 2022
Merged

Remove dead code from the TPR parser #3516

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24 changes: 0 additions & 24 deletions package/MDAnalysis/topology/TPRParser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -246,30 +246,6 @@ def parse(self, tpr_resid_from_one=True, **kwargs):

return tpr_top

# THE FOLLOWING CODE IS WORKING FOR TPX VERSION 58, BUT SINCE THESE INFO IS
# NOT INTERESTED, SO IT'S NOT COVERED IN ALL VERSIONS. PARSING STOPS HERE.

# if th.bX:
# ndo_rvec(data, th.natoms)

# if th.bV:
# ndo_rvec(data, th.natoms)

# if th.bF:
# ndo_rvec(data, th.natoms)

# not useful at the moment
# ePBC = -1;
# bPeriodicMols = False
# if th.bIr:
# # update
# data.unpack_int() # ePBC
# data.unpack_bool() # bPeriodicMols
# # 17 < 23. and ir (ir is from the c code, seems not apply here
# if th.fgen < setting.tpx_generation:
# # a crazily long (670 lines) function in c, slightly better here
# # (240 lines), so put it in setting.py
# utils.do_inputrec(data)

def _log_header(self, th):
logger.info(f"Gromacs version : {th.ver_str}")
Expand Down
306 changes: 0 additions & 306 deletions package/MDAnalysis/topology/tpr/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -353,15 +353,6 @@ def do_mtop(data, fver, tpr_resid_from_one=False):
atom_start_ndx += mt.number_of_atoms()
res_start_ndx += mt.number_of_residues()

# not useful here

# data.unpack_int() # mtop_natoms
# do_atomtypes(data)
# mtop_ffparams_cmap_grid_ngrid = 0
# mtop_ffparams_cmap_grid_grid_spacing = 0.1
# mtop_ffparams_cmap_grid_cmapdata = 'NULL'
# do_groups(data, symtab)

atomids = Atomids(np.array(atomids, dtype=np.int32))
atomnames = Atomnames(np.array(atomnames, dtype=object))
atomtypes = Atomtypes(np.array(atomtypes, dtype=object))
Expand Down Expand Up @@ -877,300 +868,3 @@ def do_blocka(data):
ndo_int(data, block_nr + 1)
ndo_int(data, block_nra)
return block_nr, block_nra


##############UTILS FOR INFORMATION NOT INTERESTED AT THE MOMENT###############

def do_grps(data): # pragma: no cover
grps_nr = []
myngrps = ngrps = setting.egcNR # remind of version inconsistency
for j in range(ngrps):
if j < myngrps:
v = data.unpack_int()
grps_nr.append(v)
ndo_int(data, v)
return grps_nr


def do_groups(data, symtab): # pragma: no cover
do_grps(data)

ngrpname = data.unpack_int()
# do_strstr, list of indices of group name: e.g. System, Protein,
# Protein-H, etc. use symtab[i] to check
ndo_int(data, ngrpname)

ngrpnr = []
grpnr = []
for i in range(setting.egcNR):
x = data.unpack_int()
ngrpnr.append(x)
if x == 0:
grpnr.append(None)
else:
l_ = []
for i in range(x):
l_.append(data.unpack_uint())
grpnr.append(l_)
# print ngrpnr
# print [len(i) for i in grpnr if i]
return


def do_atomtypes(data): # pragma: no cover
at_nr = data.unpack_int() # at: atomtype
at_radius = ndo_real(data, at_nr)
at_vol = ndo_real(data, at_nr)
at_surftens = ndo_real(data, at_nr)
at_atomnumber = ndo_int(data, at_nr)
return at_radius, at_vol, at_surftens, at_atomnumber


def do_inputrec(data): # pragma: no cover
"""Read through header information from TPR file *data* structure.

Note that this function does not return any useful data itself. If
your are interested in using the header information, use this
functions as a starting point for your own code.
"""
data.unpack_int() # ir_eI
data.unpack_int() # ir_nsteps = idum
data.unpack_int() # ir_init_step = idum =

data.unpack_int() # simulation_part
# not relevant here
# ir_nstcalcenergy = 1

data.unpack_int() # ir_ns_type
data.unpack_int() # ir_nslist
data.unpack_int() # ir_ndelta

data.unpack_real() # ir_rtpi
data.unpack_int() # ir_nstcomm
abs(data.unpack_int()) # ir_comm_mode

data.unpack_int() # ir_nstcheckpoint
data.unpack_int() # ir_nstcgsteep
data.unpack_int() # ir_nbfgscorr

data.unpack_int() # ir_nstlog
data.unpack_int() # ir_nstxout
data.unpack_int() # ir_nstvout
data.unpack_int() # ir_nstfout
data.unpack_int() # ir_nstenergy
data.unpack_int() # ir_nstxtcout

data.unpack_real() # ir_init_t = rdum =
data.unpack_real() # ir_delta_t = rdum =

data.unpack_real() # ir_xtcprec
ir_rlist = data.unpack_real()

data.unpack_int() # ir_coulombtype
data.unpack_real() # ir_rcoulomb_switch
ir_rcoulomb = data.unpack_real()

data.unpack_int() # ir_rvdwtype
data.unpack_real() # ir_rvdw_switch
ir_rvdw = data.unpack_real()

max(ir_rlist, max(ir_rvdw, ir_rcoulomb)) # ir_rlistlong

data.unpack_int() # ir_eDispCorr
data.unpack_real() # ir_epsilon_r
data.unpack_real() # ir_epsilon_rf

data.unpack_real() # ir_tabext

data.unpack_int() # ir_gb_algorithm
data.unpack_int() # ir_nstgbradii
data.unpack_real() # ir_rgbradii
data.unpack_real() # ir_gb_saltconc
data.unpack_int() # ir_implicit_solvent

data.unpack_real() # ir_gb_epsilon_solvent
data.unpack_real() # ir_gb_obc_alpha
data.unpack_real() # ir_gb_obc_beta
data.unpack_real() # ir_gb_obc_gamma

# not relevant here
# ir_gb_dielectric_offset = 0.009
# ir_sa_algorithm = 0 # esaAPPROX

data.unpack_real() # ir_sa_surface_tension

data.unpack_int() # ir_nkx
data.unpack_int() # ir_nky
data.unpack_int() # ir_nkz
data.unpack_int() # ir_pme_order
data.unpack_real() # ir_ewald_rtol
data.unpack_int() # ir_ewald_geometry

data.unpack_real() # ir_epsilon_surface

data.unpack_bool() # ir_bOptFFT
data.unpack_bool() # ir_bContinuation
data.unpack_int() # ir_etc

# not relevant here
# ir_nsttcouple = ir_nstcalcenergy

data.unpack_int() # ir_epcpressure coupling
data.unpack_int() # ir_epctepctype, e.g. isotropic

# not relevant here
# ir_nstpcouple = ir_nstcalcenergy
data.unpack_real() # tau_p

data.unpack_farray(setting.DIM, data.unpack_real) # ir_ref_p_XX
data.unpack_farray(setting.DIM, data.unpack_real) # ir_ref_p_YY
data.unpack_farray(setting.DIM, data.unpack_real) # ir_ref_p_ZZ

data.unpack_farray(setting.DIM, data.unpack_real) # ir_compress_XX
data.unpack_farray(setting.DIM, data.unpack_real) # ir_compress_YY
data.unpack_farray(setting.DIM, data.unpack_real) # ir_compress_ZZ

data.unpack_int() # ir_refcoord_scaling
data.unpack_farray(setting.DIM, data.unpack_real) # ir_posres_com
data.unpack_farray(setting.DIM, data.unpack_real) # ir_posres_comB

data.unpack_int() # ir_andersen_seed
data.unpack_real() # ir_shake_tol
data.unpack_int() # ir_efep

data.unpack_real() # ir_init_lambda = rdum =
data.unpack_real() # ir_delta_lambda = rdum =

# Not relevant here
# ir_n_flambda = 0
# ir_flambda = None

data.unpack_real() # ir_sc_alpha
data.unpack_int() # ir_sc_power
data.unpack_real() # ir_sc_sigma

# not relevant here
# ir_sc_sigma_min = 0
# ir_nstdhdl = 1
# ir_separate_dhdl_file = 0 # epdhdlfileYES;
# ir_dhdl_derivatives = 0 # dhdlderivativesYES
# ir_dh_hist_size = 0
# ir_dh_hist_spacing = 0.1

data.unpack_int() # ir_eDisre
data.unpack_int() # ir_eDisre_weighting
data.unpack_bool() # ir_bDisreMixed

data.unpack_real() # ir_dr_fc
data.unpack_real() # ir_dr_tau
data.unpack_int() # ir_nstdisreout

data.unpack_real() # ir_orires_fc
data.unpack_real() # ir_orires_tau
data.unpack_int() # ir_nstorireout

data.unpack_real() # ir_dihre_fc

data.unpack_real() # ir_em_stepsize
data.unpack_real() # ir_em_tol

data.unpack_bool() # ir_bShakeSOR
data.unpack_int() # ir_niter

data.unpack_real() # ir_fc_stepsize

data.unpack_int() # ir_eConstrAlg
data.unpack_int() # ir_nProjOrder
data.unpack_real() # ir_LincsWarnAngle
data.unpack_int() # ir_nLincsIter

data.unpack_real() # ir_bd_fric
data.unpack_int() # ir_ld_seed

ndo_rvec(data, setting.DIM) # ir_deform

data.unpack_real() # ir_cos_accel

data.unpack_int() # ir_userint1
data.unpack_int() # ir_userint2
data.unpack_int() # ir_userint3
data.unpack_int() # ir_userint4
data.unpack_real() # ir_userreal1
data.unpack_real() # ir_userreal2
data.unpack_real() # ir_userreal3
data.unpack_real() # ir_userreal4

# pull_stuff
data.unpack_int() # ir_ePull

# grpopts stuff
ir_opts_ngtc = data.unpack_int()
# not relevant here
# ir_opts_nhchainlength = 1

ir_opts_ngacc = data.unpack_int()
ir_opts_ngfrz = data.unpack_int()
ir_opts_ngener = data.unpack_int()

ndo_real(data, ir_opts_ngtc) # ir_nrdf
ndo_real(data, ir_opts_ngtc) # ir_ref_t
ndo_real(data, ir_opts_ngtc) # ir_tau_t

if ir_opts_ngfrz > 0:
ndo_ivec(data, ir_opts_ngfrz) # ir_opts_nFreeze

if ir_opts_ngacc > 0:
ndo_rvec(data, ir_opts_ngacc) # ir_opts_acc

ndo_int(data, ir_opts_ngener ** 2) # ir_opts_egp_flags
ndo_int(data, ir_opts_ngtc) # ir_opts_annealing
ir_opts_anneal_npoints = ndo_int(data, ir_opts_ngtc)

ir_opts_anneal_time = []
ir_opts_anneal_temp = []
for j in range(ir_opts_ngtc):
k = ir_opts_anneal_npoints[j]
ir_opts_anneal_time.append(ndo_int(data, k))
ir_opts_anneal_temp.append(ndo_int(data, k))

# Walls
data.unpack_int() # ir_nwall
data.unpack_int() # ir_nwall_type
data.unpack_real() # ir_wall_r_linpot

# ir->wall_atomtype[0], ir->wall_atomtype[1]
ir_wall_atomtype = []
ir_wall_atomtype.append(data.unpack_int())
ir_wall_atomtype.append(data.unpack_int())

# ir->wall_density[0], ir->wall_density[1]
ir_wall_density = []
ir_wall_density.append(data.unpack_real())
ir_wall_density.append(data.unpack_real())

data.unpack_real() # ir_wall_ewald_zfac

# cosine stuff for electric fields
ir_ex_n, ir_et_n, ir_ex_a, ir_ex_phi, ir_et_a, ir_et_phi = [], [], [], [], [], []
for j in range(setting.DIM):
x = data.unpack_int()
ir_ex_n.append(x)
y = data.unpack_int()
ir_et_n.append(y)

ir_ex_a.append(ndo_real(data, x))
ir_ex_phi.append(ndo_real(data, x))
ir_et_a.append(ndo_real(data, y))
ir_et_phi.append(ndo_real(data, y))

# QMM stuff
data.unpack_bool() # ir_bQMMM
data.unpack_int() # ir_bQMMMscheme
data.unpack_real() # ir_scalefactor
data.unpack_int() # ir_opts_ngQM

# if ir_opts_ngQM > 0:
# do_something

# indicating the parsing finishes properly
data.done()