Gdtyjr

I have some problems in spacing.
I just want to put equations in the text.
What I found is that the vertical spacing between the equation and text is not consistent.
Some is large and some is small. Both spacings above and below equation are not consistent.
How do I get consistent spacing in the entire thesis?
I can adjust spacing using vspacebaselineskip.
But I am not sure the spacing is exactly the same or not. It doesnt seems good solution.
Here is my code.

documentclass[twoside]utmthesis
%According to the new manual, should not mixed single-side with two-side 
printing
usepackagegraphicx
usepackageurl 
%usepackage[pages=some]background
usepackagelipsum
usepackagepdflscape
usepackageverbatim
usepackagetextcomp
usepackagemhchem
usepackageamsmath 
usepackagelistings
usepackagegraphicx
usepackagemwe
usepackagexr
usepackagesiunitx
usepackagefloat
usepackagesubfig
newsaveboxbigleftbox
usepackagetikz
usepackagenameref
%usepackage[printonlyused]acronym
usepackageromannum
usetikzlibraryshapes.geometric, arrows
usepackagenatbib
letcitecitep
bibliographystyleutmthesis-authordate

begindocument
subsection1D numerical modeling of the SI-engine
vspacebaselineskip
The numerical models and related equations applied in the 1D engine 
simulation are presented and briefly discussed.
subsubsectionPipe
vspacebaselineskip
In one-dimension modeling of flow through the pipes, working fluid is 
assumed that it is flowing in one-direction, instead of three direction (X, 
Y, and Z). It seems plausible, as most fluid particles are moving mostly in 
longitudinal direction rather than radial direction of the pipe. A one- 
dimensional pipe flow is described by Euler equation which is given in 
conservation form below.

beginequation labelEuler
fracpartial mathbfUpartial t + fracpartial mathbfF(U) 
partial x= mathbfS(U)
endequation

$textbfU$ and $textbfF$ represent state vector and flux vector, 
respectively which are represented as follows.

beginequation
mathbfU= beginpmatrix
rho \
rho cdot u \
rho cdot barC_v cdot T + frac12 cdot rho cdot u^2 \
rho cdot w_j endpmatrix,,, , ,,, mathbfF= beginpmatrix
rho cdot u \
rho cdot u^2 + p \
rho cdot (E+p) \
rho cdot u cdot w_j endpmatrix
endequation

With total energy, $E$ is given as below.

beginequation labelE
beginsplit
E=rho cdot barC_v cdot T + frac12 cdot rho cdot u^2
endsplit
endequation

The source term, $textbfS$ is divided into two different sub-source 
terms. 

beginequation labelS
 mathbfS(U)= mathbfS_A(F(U)) + mathbfS_R(U)
endequation

$mathbfS_A$ is the source term caused by axial changes in the pipe cross 
section.

beginequation labelSa
mathbfS_A(F(U))= - frac1A cdot fracdAdx cdot left(F + 
beginpmatrix
0 \
-p \
0 \
0 
endpmatrix right)
endequation

$mathbfS_R$ is the source term taking into account homogeneous chemical 
reaction, friction, heat and mass transfer between gas and solid phase.

beginequation labelSr
mathbfS_R(F(U))= beginpmatrix
0 \
-fracF_RV \
fracq_wV \
M W_j cdot left(sumlimits_i^R_hom nu_i.j cdot 
dotr_iright)endpmatrix
endequation

bibliographyreference
enddocument