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Chapter 4: Methodology
4.0 INTRODUCTION TO CHAPTER 4
The project is divided into three parts, field work, laboratory work and
basin modelling. Fieldwork was conducted by detail mapping of the study area.
Outcrops were logged and standard procedure of collecting sample was carried
out. In the next stage, laboratory work was performed to evaluate source rocks
properties. The final step was to run the basin modelling by integrating the results
of the laboratory analyses and field mapping data. Figure 4.1 summarized the
methodology used in this project.
Fieldwork mapping and
collecting samples
Laboratory work
Source
Rocks
Evaluation
TOC
Analyzer
Rock Eval
Pyrolysis
Reconstruction of
Paleodepositional
Environment
Thermal
Maturity
Assessment
Hydrocarbon
Characterizations
VR
Bitumen Extraction
Tmax
Column
Chromatography
Palynology
Micropaleontology
Py-GC
Biomarkers
GC-MS analysis
Maceral
Analyses
Basin Modelling
Conclusion
Figure 4.1. Summary of the methodology were performed in this study.
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Chapter 4: Methodology
4.1 FIELDWORKS
Two field work sessions were conducted in 2006. This field work involved
detail mapping of sedimentology, structural, and stratigraphy. Selected outcrops
were logged and the location of the samples taken within the stratigraphic interval
was marked. Unweathered samples of 10cm X 10cm X 10cm were taken with
weathered surfaces were scrapped away to avoid contamination. Samples location
and structural data were located on maps with the aid of Garmin Global Positioning
System (GPS). Outcrops locations were transferred to a digitized base map (Figure
1.2). A detailed listing of outcrop location is in Appendix 1.
4.2 LABORATORY WORKS
Laboratory
work
was
performed
on
coal,
coaly
sediment
and
carbonaceous mudstone and other organic rich rocks from the Ganduman
Formation and Sebahat Formation. More than 30 samples from the organic rich
rocks were analyzed in order to determine source rock quality. However, poor
organic rocks (of probable reservoir rocks) such as sandstone and limestone also
were evaluated to identify the possible occurrence of migrated hydrocarbons,
which is useful for oil to source rock correlation. The source rock evaluation
included petrological and geochemical analyses.
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Chapter 4: Methodology
4.2.1 ORGANIC PETROLOGY
4.2.1.1 Polished Block Preparation
Rock samples were crushed into small pieces (2-3mm) using pastel and
mortar. Samples then were, embedded in 30 mm latex moulds with liquid epoxy
resin and hardened for 48 hours at 30°C. Samples were then gradually ground with
350 (coarse), 550 (intermediate), 800 (fine), 1200 (very fine) abrasive powder and
finally polished with 1µm alumina powder-deagglomerate, 0.3 µm alumina powderdeagglomerate, and 0.04 µm OP-S suspension solution for final polishing. Figure
4.2 (a) shows tools and apparatus that are being used for preparing mount block
samples and Figure 4.2 (b) shows the ready-made sample for analsis. The
polished sample was quality-checked by observing under microscope and should
have flat and smooth surface, as any scratches can influence the vitrinite
reflectance measurements.
a.
Serifix
Resin
b.
Oil
Cup and
stick
Pastel and
mortar
Saphire refective
index
Samples
Hardener
Mould
cups
Figure 4.2. (a) Tools and chemicals that are being used for preparing mount blocks
(b) prepared polish-blocks, refractive index, and oil immersion for petrographic
analysis.
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Chapter 4: Methodology
4.2.1.2 Maceral Analyses and Vitrinite Reflectance
For a detailed study of the composition of the organic matter (OM), a
qualitative and quantitative microscopic study of the phytoclasts in shale and
macerals in coal was carried out on selected organic rich samples. Thirty-three
samples of various lithologies were studied. A Leica CTR6000M microscope was
used for this petrographic purpose (Figure 4.3). Microscopic examination was
carried out principally in oil immersion under reflected white light and UV light.
A Leica CTR6000M microscope was utilized for macerals analysis as it is
equipped with high-resolution camera and gives an appropriate picture under UV
light. Macerals point counting was carried out by a semi-automatic technique using
Diskus Maceral software. 150 µm X 150 µm distance interval was used to be
carried out on the highly heterogeneous maceral, whereas, for the less
heterogenous maceral, 200 µm X 200 µm distance interval was used. These
measurements were carried on coal samples. As for mudstone samples, the
amount of phytoclasts were approximately averaged due to low concentration of
phytoclasts. The classification of coal macerals and macerals groups are based on
ICCP (1963, 1971, 1975) and macerals subgroups by Australian Standard 2856
(1986).
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Chapter 4: Methodology
The vitrinite reflectance measurement was carried upon calibration using
Leica CTR6000M using Diskus Fossil software. The measurements were carried
out after calibrated using standard sapphire refractive indices (0.589 %). A total of
30 measurements for Dispersed Organic Matter (DOM) and 50-100 measurements
on coals (Pawlewicz and Barker, 1994) with good agreement to two decimal places
of the VR value. The measurements were carried out under white light using an oil
immersion X50 objective. The aperture size at measured point can be changed to
the smallest of 3 µm for phytoclasts and the biggest size 20 µm for homogenous
band of vitrinite. The smaller aperture size is substantially important used in shale
when measuring vitrinite reflectance, as plant fragment is very tiny and dispersed.
Figure 4.3. Leica CTR6000 Photometry Microscope.
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Chapter 4: Methodology
4.2.2 ORGANIC GEOCHEMSITRY
4.2.2.1 Bitumen extraction (Soxhlet Extraction Procedure).
Fresh outcrop samples were cleaned with a wire brush or penknife to
remove contaminated surfaces. The samples were crushed into powder form using
solvent-rinsed morta and pestel. An empty thimble was weighed and an
approximately 2/3 of thimble filled with powdered rock sample and capped with
cotton wool. Then, the thimble that filled with sample was weighed and placed into
a Soxhlet extractor. The solvent (mixture of dichloromethane and methanol in ratio
93:7) was prepared in a measuring cylinder and add to a round bottom flask
together with anti-bumping granule and copper sheet. The Soxhlet extractor was
attached to the round bottom flask and connected to a condenser connection were
ensured to be firmed. The heater was turned on to about 3/4 of the maximum
temperature while the water was ensured to be flowed through the condenser. The
heating temperature was reduced to 1/3 of maximum once the solvent was boiling.
The samples were extracted at minimum time for about 12 hours to a maximum of
5 days. The extracted Extractable Organic Matter (EOM) was collected in 250 mL
round bottom flask. Subsequently, solvent was evaporated using Buchi rotary
evaporator. Final elute EOM was collected in large vial. Figure 4.4 shows the stage
of EOM extraction using soxhlet extractor, stage of solvent evaporation using
rotary evaporator, and stage of collecting EOM into vial.
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Chapter 4: Methodology
a) EOM
extraction
from rock
Condenser
Water
circulation
Soxhlet
Thimble+Sample
Round bottom flask
+solvent+copper sheet+
anti bumping granule
Heating Mantle
b) EOM
Evaporation
c) Collecting
EOM
Figure 4.4. a) Stage of EOM extraction using soxhlet extractor; b) stage of solvent
evaporation using rotary evaporator; c) stage of collecting EOM into vial.
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Chapter 4: Methodology
4.2.2.2 Hydrocarbon Fractionation Technique
4.2.2.2.1 Column Chromatography
The hydrocarbon fractions were separated using a glass column (30 cm x
0.75 cm i.d.), packed with approximately 20 cm of silica gel (BDH 60-120 mesh),
supported by a 2-3 cm layer of alumina. The silica was slurry-packed using light
petroleum (Bp 40-60°C) by gently knocking the column using rubber rod, whilst the
alumina was gravity-packed. While packing, avoided air bubbles from being
trapped in the packed column. A known quantity, approximately 50-100 mg of the
extract was dissolved using small quantity of dichloromethane, adsorbed on to
alumina. The dichloromethane was removed using a stream of nitrogen and the
absorbed extract was added to the top of the column.
The column was then developed with solvents of increasing polarity, i.e.
light petroleum (100 ml), dichloromethane (100 ml) and methanol (50 ml)
successively. The elutes were collected in separate 250 ml round-bottom flasks.
The solvents were later reduced by Buchi evaporation and the weighed of elutes
were recorded. The recovered elute was transferred into 3 vials i.e. aliphatic,
aromatic and Nitrogen-Sulphur-Oxygen (NSO) compounds. The vial was blown to
dryness under a stream of
Oxygen Free Nitrogen (OFN) and weighed. The
aliphatic fraction then diluted with petroleum ether and analyzed using gas
chromatography (GC) or gas chromatography-mass spectrometry (GC-MS). Three
stages are shown in Figure 4.5.
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Chapter 4: Methodology
Column
Chromatography
Long column
1cm Alumina
15cm Silica
gel
Hydrocarbon
Fraction
Hydrocarbon
Evaporation
Collected
Hydrocarbon
Fractions
Figure 4.5. The stages of collecting hydrocarbon fractionation by column
chromatography, started with separation of 3 hydrocarbon fractions using column
chromatography, followed by solvent evaporation stage using rotary evaporator,
and stage of collecting hydrocarbon fraction into small vial.
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Chapter 4: Methodology
4.2.2.2.2 Thin Layer Chromatography (TLC)
The glass plates (20 cm X 20 cm) were cleaned with distilled water to
remove contamination and were then oven dried. The glass plates were rinsed in
methanol before use to remove any subsequent contamination and were placed on
a plate leveler. A slurry of approximately 35 g of silica (Merck Kiesed gel G nach
type 60) and 70 ml of distill water was then prepared. The slurry was quickly
spread across the plate with a 0.5mm coating and allowed to set. The slurred
plates were then heated in an oven of 110 °C for at least 2 hours.
Before use, the slurred plates were soaked in ethyl acetate to remove any
contamination and then reactivated for at least 1 hour in oven. After the plates
were completely dry, the extractable organic matter (approximately 25mg) was
diluted with dichlomethane (DCM) and spotted (using a fine point-pipette) in a
straight line approximately 2 cm from the bottom of plate and bottom-soaked with
light petroleum (Petroleum ether - 40° - 60° C) in a glass plate (Figure 4.6).
The plates were viewed under ultra-violet light to see the hydrocarbon
fraction bands. If the hydrocarbons separation does not show any distinctive
bands, the plates were then sprayed with a methanolic solution of Rhodamine 6G
and viewed under ultra-violet light. The band containing the saturated
hydrocarbons, which has a Rf value (ratio of the distance of solute from origin to
distance of solvent front from origin) of approximately 70-80% was scraped off.
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Chapter 4: Methodology
The hydrocarbons were recovered from the scraped off band by elution with
50 ml light petroleum: DCM (40:10) using a short columns containing a layer of
approximately 1-2 cm of alumina. The aromatic was recovered by eluting with
petroleum: DCM (30:30), and NSO compound with methanol.
The solvent was evaporated, but not to dryness, using a rotary evaporator.
The recovered elute was transferred into vials. The vials were blown to dryness
under a stream of Oxygen Free Nitrogen (OFN) and weighed. It was then diluted
with petroleum ether and analyzed using gas chromatography (GC) or gas
chromatography-mass spectrometry (GC-MS). The main stages are shown in
Figure 4.6.
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Chapter 4: Methodology
a
b
Plate’s Leveler
Plates with slurry
silica gel
Ethyl Acetate
c
d
Short
Column
1cm
Alumina
Samples with
methanolic
Rhodemine
Petroleum Ether
Hydrocarbon
Fraction
Figure 4.6. The stages used in thin layer chromatography; a) preparation of plate
leveler slurred plates on plate leveler, b) plates soaking into ethyl acetate, c) plates
soaking in Petroleum ether after spotted by EOM, d) stage of hydrocarbon
separation.
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Chapter 4: Methodology
4.2.3 Gas Chromatography - Mass Spectrometry (GC-MS).
Gas Chromatography - Mass Spectrometry (GC-MS) analyses were
performed on an Agilent Gas Chromatograph 6890N combined with 5975 Inert
Mass Selective Detector (Figure 4.7). An approximately of 1 µL of the prepared
saturated hydrocarbon fractions were injected to the gas chromatogram using
Agilent gold standard syringe.
The hydrocarbon compounds were separated on a 30 m X 250 µm X 0.25
µm fused silica capillary column. The GC temperature was programmed from 40
C to 300 0C (30 min hold) at 4 °C min−1 in an oven for 95 minutes. The injected
0
fractions were vaporized and mixed with helium as a carrier gas. The separated
compounds were transferred to the source of the mass spectrometer where they
were ionized by an electron beam. The fingerprints of the mass fragmentograms
were then obtained with graph peak as shown in Appendix 6. Figure 4.8 shows the
programmed temperature which was used during the GC-MS analysis.
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Chapter 4: Methodology
b
a
Figure 4.7. a) Gas chromatography system; b) Mass-spectrometer
Figure 4.8. The setting of the gas chromatography performed in this study.
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Chapter 4: Methodology
4.2.4 Pyrolysis-Gas Chromatography (Py-GC)
Pyrolysis-Gas Chromatography (Py-GC) analysis was performed using a
Double-Shot Pyrolyzer Py-2020iD from Frontier Laboratories Ltd (Figure 4.8-b). A
temperature programmed pyrolysis technique (Py-GC) was carried out for ten
selected samples with high TOC and HI values. Most of the analyzed samples ere
coals. At least 10-20mg of fine ground whole rock sample was placed in a sample
probe as shown in Figure 4.8-a. Under the desorption programme, the sample
probe was lowered into the furnace and heated at 53°C initial temperature under
the flow of nitrogen, hydrogen and compress air. The temperature then was
increased at rate 20°C/min until 300°C and held at the temperature for 15 minutes.
After the desorption programme was finished, the sample probe was pushed to the
upper part of the furnace column. The sample was pyrolyzed from 300°C to 600°C
at 20°C/min for 95 minutes. As a result, the volatile matter and free hydrocarbons
were pyrolyzed to form the first shot peaks. After the first shot finish, under
pyrolysis programme, the sample probe was dropped into interface column. The
sample was pyrolysed at a constant 600°C at 20°C/min in a tube furnace type
pyrolyzer interface to an Aggilent Gas Chromatograph 6890N for 95 minutes
(Figure 4.8-c). The outlet of the pyrolyzer was connected to a fused silica capillary
column (30 m x 250 µm x 0.25 µm) via an interface/splitter (sample/split ratio;
1:30). The outlet of the splitter was connected to a flame ionisation detector (FID)
and the course of the pyrolysis could be followed by the detector response of the
bulk pyrolysis product that was recorded as a broad second shot peak. The
settings for the pyrolyzer and the sequence programme are shown in figure 4.9
and 4.10 respectively.
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Chapter 4: Methodology
b
a
c
Figure 4.8 a) Sample probe of the Py-GC attached to the back inlet; b) DoubleShot Pyrolyzer Py-2020iD; c) Gas chromatography.
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Chapter 4: Methodology
Figure 4.9. Setting of the double-shot pyrolyses programme.
300°C to
600°C at
20°C/min
600 °C
Auto
cooling
53°C to
300°C at
20°C/min
53°C
300 °C
Auto
cooling
15 min
95 min
95 min
Desorption
Pyrolysis
Figure 4.10. Setting programme in Double-Shot Analysis.
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Chapter 4: Methodology
4.2.5 Leco TOC, Rock Eval-6 and Source Rock Analyzer.
These analyses were carried out in Geological Survey of Denmark and
Greenland (GEUS) and PETRONAS Research and Technology Division. A total of
33 prospective source rock samples were selected for detailed analyses. For pretreatment, the contaminated surfaces were removed with wire brush and penknife
and were subsequently crushed into powder. The powdered samples were then
wrapped into aluminums foil, labelled and sealed to avoid any contaminations.
All the prepared samples were analyzed using standard methods. For TOC
determination, previous methods by Espitalié, et. al., (1985) and Lafargue, E., et.
al., (1998) were followed, using the Leco TOC analyzer. To determine the kinetics
of kerogen cracking, the source rock samples were analyzed using the Source
Rock Analyzer and Rock-Eval 6. Small quantities (10–100 mg) of powdered rock
samples were pyrolyzed. The calibration of SRA using the IFP 160000 standard
and in-house Marl Slate standard were performed for control every 10 samples.
Results are summarized in section 6.1, chapter 6.
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Chapter 4: Methodology
4.2.6 Fourier Transform Infrared (FTIR)
Fourier Transform Infrared (FTIR) analysis was perfomed in two different
modes which are spectroscopy and attenuated total reflection (ATR) through
different samples preparation (powder and polish block). The ATR method was
performed on the powder samples whereas spotlight imaging used mounted polish
blocks samples.
The spotlight imaging methods were carried out on polished coal samples
under reflected light using Perkin Elmer Spectrum 300 Spotlight FTIR-Microscope
(Figure 4.11-a). Selected samples that possess liptinite rich maceral were analysed
to determine the chemical variation according to the absorption energy. The FTIR
measurements were carried out at 25°C on a Perkin Elmer Spectrum FTIR
spectrometer equipped with a Spotlight Image detector at a resolution of 4 cm–1,
using a gold plate as background (Figure 4.12). Interferograms from 240 scans
were averaged to obtain one spectrum. Liquid nitrogen was constantly pumped into
the spectrometer to minimize water vapor, which absorbs in the spectral region of
interest. The spectral line in the region of interest is in range 4000 cm-1 to 650 cm-1.
A program Spectrum was used for spectral deconvolution, curve fitting and
determination of peak integration areas. However, the result cannot be displayed
here due to poor quality of peak obtained as the machine is still in calibration.
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Chapter 4: Methodology
The Attenuated Total Reflection-FTIR (ATR-FTIR) was performed on a
Perkin Elmer Spectrum-100 FTIR Spectrometer (Figure 4.11-b). The spectrometer
is equipped with a universal ATR unit, carried out on the powder samples that were
prepared after crushing with pastel and mortar. The powdered sample was placed
on a Diamond/ZeSe crystal plate and was compressed below 98%. Attenuated
total reflection-FTIR measurements were performed at 25°C. Interferograms from
240 scans were averaged to obtain one spectrum by overlain the background of
the spectrum (Figure 4.13).
a
b
Figure 4.11. (a)The Spectrum 300 Spotlight FTIR-Microscope used for imaging and
maceral mapping under reflected light; (b) Spectrum-100 FTIR Spectrometer used
for powder samples using universal ATR sampling accessory.
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Chapter 4: Methodology
Figure 4.12. Scanned background of gold plate.
13.1
12
11
10
9
8
EGY 7
6
5
4
3
2
1.2
4000.0
3600
3200
2800
2400
2000
1800
cm-1
1600
1400
1200
1000
800
650.0
Figure 4.13. Background spectrum of ATR.
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Chapter 4: Methodology
4.3 PALYNOLOGY PROCEDURE
Standard palynological processing was carried out using as described by Wood et.
al., (1996), with the help of technical staff of PETRONAS Research Sdn. Bhd. The
detail workflow is described below.
A. Crushing rock samples
Fresh outcrop samples were cleaned from contamination by scrapping off
any weathered surface using a pen knife. Approximately 10-15 mg was crushed
using morta and pestel into silt size. Prepared samples were then kept in sample
container and labelled.
B. Separation from carbonate
The samples were treated with 10% hydrochloric acid in the plastic
centrifuge tubes to remove the carbonates. The tubes were then 2/3 filled with
distill water and spinned with centrifuge rotator. The top of water layer was
removed. The sequence was repeated 3 times to ensure the acid was completely
removed.
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Chapter 4: Methodology
C. Separation from clastic
The decarbonated samples were treated with hydrofluoric acid (48-68%)
and stirred using spatula to remove clastic particles. The samples were then left
overnight to ensure the clastic fraction was completely removed and suspended to
the clay layer. The above layer was transferred into a centrifuge tube and filled with
distilled water and rotated for 5 minutes in a centrifuge. This process was repeated
for 5 times. The sample was treated with a concentrated hot bath of hydrochloric
acid, 1:1 (HCL: distill water) to remove any remnants of Ca+ ions. Samples were
allowed to cool and were then washed with distilled water and centrifuged (1500
rpm) to remove the upper layer. This was repeated for 5 times. A mixture of ZnBr
(1 kg: 370 mL distilled water) with specific gravity 2.2 was prepared. The ZnBr was
poured into the centrifuge tube and was left overnight. The residue (upper part)
which contains the pollen were sucked with pipette and washed with distilled water.
D. Slide preparation
The final residue product was mounted on the thin section slides and labelled.
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Chapter 4: Methodology
4.4 FORAMINIFERA ANALYSES
The foraminiferas analysis was performed by the technical staff from
PETRONAS Research and Technology Division. The procedure used follows
Cushman (1950). A total of 8 samples collected from fieldwork have been analysed
for foraminifera. 50g of sample were weighed and processed. Simple soaking
procedure first required to dilute the mud and organic elements in samples.
Unconsolidated sediment and some soft rocks like mud and shale samples are
easily disaggregated after soaking in water for a few hours, whereas harder rocks
may first require crushing before soaking. In the case of samples are more
resistant, additional treatment is used which, 3% of Hydrogen Peroxide (H 2O2)
concentration has been added into immersion samples to isolate the preserve
foraminifera specimens from sediment grains surround them.
Once the sediments have been dispersed, samples were washed through a
standard sieve with mesh openings of 63 microns under a gentle stream of water.
This process was eliminated all the mud and organic elements in samples and
trapped the residue sediments mix foraminifera fossil in sieve. Then, the residue
dried in oven with constant temperature within 40 to 50°C for about 24 hours.
Labelling is carefully transcribed during sample preparation. All residues were then
segregated to different grain size range using the following mesh sizes: 500 – 250
µm, 250 – 125 µm, 125 – 63 µm and <63 µm. All specimens were picked and
counted under the microscopic examination.
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Chapter 4: Methodology
4.5 BASIN MODELLING
This study was carried out using Integrated Exploration Systems (IES)’s
Petromod basin modeling software package (version 10.0 SP1), donated by
Coordinating Committee for Geoscience Programmes in East and South East Asia
(CCOP)
during
the
Institutional
Capacity
Building
(ICB-CCOP1)
project
implementation. The software package includes 1D, 2D, and 3D modules, although
only the 1D and 2D were used in this investigation. The burial history and thermal
maturity were modeled using the 1D software, whereas hydrocarbon generation,
migration and accumulation modelling used the 2D module. The geometry of the
basin, basin fill and stratigraphy are based on a geological cross section from a
previous study (ISIS, 2005; provided by PETRONAS). The provided cross section
was scanned and the scanned image was imported into Petromod software and
digitized. The digitized section was then gridded into a geocellular model. All the
input data such as age, lithology, TOC and HI data were the inserted using age
assignment, facies definition, and facies assignment tables.
Subsequent to the digitizing and gridding the section, the model was
simulated using hybrid migration method (Darcy’s + Flow Path). The output of the
model is displayed in a 2D Viewer. A vertical depth extraction point from the 2D
viewer was extracted at the deepest location within the basin and displayed in a 1D
Viewer. The vitrinite reflectance and bottom hole temperature curves as displayed
in 1D viewer were calibrated to the selected offshore wells data. The best fit
calibration curve model was used for interpretation and display in 2D viewer. A
badly fitting calibration curve must be adjusted by modifying the heat flow history
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Chapter 4: Methodology
by applying geologically plausible heat flow values. The diagram as shown in
Figure 4.14 describes the workflow to construct the 2D basin model and extracted
1D model.
Scan image and import as a background
Digitize the cross-section based on the
background image
Grid current section
Insert the input parameters (e.g. age, lithology,
TOC, HI)
Simulate model using hybrid migration method
Display in 2D Viewer
Depth extraction of a vertical line from 2D
Viewer in the selected location within the
basin.
CALIBRATION
OUTPUT
Calibrate the model curve with VR and BHT
data from selected offshore wells in 1D Viewer
extraction
Reopen the 2D Viewer and display the output
Figure 4.14. Summary of the basin modelling work flow using IES Petromod
version 10.0 SP1.
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